Refactor all *.from_db() routines to use from_db_json() #821
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## dev #821 +/- ##
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+ Coverage 79.04% 79.15% +0.11%
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Files 161 161
Lines 13607 13593 -14
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+ Hits 10755 10759 +4
+ Misses 2852 2834 -18 ☔ View full report in Codecov by Sentry. |
This wrapper calls json.loads() but also handles None (returning None), which enables the code at many call sites to be simplified. Removed some callers' `if isinstance(field, str): ...` code, which has the effect of newly disallowing field values that are already dicts. However we've verified that all *.from_db() calls have raw database outputs as their arguments, so such fields will be always be strings and IMHO giving a dict to from_db_json() is really a logic error that should be detected. In SequencingGroupInternal.from_db() added `pop(..., None)` so that a missing meta field is now accepted. The previous code suggests that having pop() produce KeyError here was unintended. The expected argument types for from_db_json() are listed in the definition, but we don't list its return type. The best we could say in general is `object` but most call sites expect `dict[str, str]` (or occasionally `list[str]`) due to the shape of their expected JSON. Specifying `object` would lead to mypy errors at these call sites.
Expands test coverage to include audit_log.py from_db_json change.
Merged
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Stacked on top of PR #659 (but for merging into dev after that one has been merged), this refactors existing code to use
from_db_json(), newly added in the multiple external-ids PR.This wrapper calls json.loads() but also handles None (returning None), which enables the code at many call sites to be simplified.
Removed some callers'
if isinstance(field, str): ...code, which has the effect of newly disallowing field values that are already dicts. However we've verified that all *.from_db() calls have raw database outputs as their arguments, so such fields will be always be strings and IMHO giving a dict to from_db_json() is really a logic error that should be detected.In SequencingGroupInternal.from_db() added
pop(..., None)so that a missing meta field is now accepted. The previous code suggests that having pop() produce KeyError here was unintended.The expected argument types for from_db_json() are listed in the definition, but we don't list its return type. The best we could say in general is
objectbut most call sites expectdict[str, str](or occasionallylist[str]) due to the shape of their expected JSON. Specifyingobjectwould lead to mypy errors at these call sites.I suppose we could have a
dict_from_db_json()routine for the common case of metadict[str,str]expansion that could have that return type annotation and could even validate that the JSON was of the expected form! But I think that would be overkill…