Closed Jay-sanjay closed 7 months ago
Attention: 7 lines
in your changes are missing coverage. Please review.
Comparison is base (
5a0a09a
) 73.81% compared to head (8864f30
) 74.51%.
Files | Patch % | Lines |
---|---|---|
src/getters.jl | 80.00% | 7 Missing :warning: |
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Yea, I just tried testing this and here is what I see:
GetCohortSubjects Tests: Error During Test at /home/thecedarprince/FOSS/OMOPCDMCohortCreator.jl/test/sqlite/getters.jl:405
Got exception outside of a @test
BoundsError: attempt to access 0-element Vector{Union{Missing, Float64}} at index [1:8]
Stacktrace:
[1] throw_boundserror(A::Vector{Union{Missing, Float64}}, I::Tuple{UnitRange{Int64}})
@ Base ./abstractarray.jl:744
[2] checkbounds
@ ./abstractarray.jl:709 [inlined]
[3] getindex(A::Vector{Union{Missing, Float64}}, I::UnitRange{Int64})
@ Base ./array.jl:921
[4] macro expansion
@ ~/FOSS/OMOPCDMCohortCreator.jl/test/sqlite/getters.jl:412 [inlined]
[5] macro expansion
@ ~/.julia/juliaup/julia-1.9.3+0.x64.linux.gnu/share/julia/stdlib/v1.9/Test/src/Test.jl:1498 [inlined]
[6] top-level scope
@ ~/FOSS/OMOPCDMCohortCreator.jl/test/sqlite/getters.jl:407
[7] include(fname::String)
@ Base.MainInclude ./client.jl:478
[8] macro expansion
@ ~/FOSS/OMOPCDMCohortCreator.jl/test/runtests.jl:51 [inlined]
[9] macro expansion
@ ~/.julia/juliaup/julia-1.9.3+0.x64.linux.gnu/share/julia/stdlib/v1.9/Test/src/Test.jl:1498 [inlined]
[10] macro expansion
@ ~/FOSS/OMOPCDMCohortCreator.jl/test/runtests.jl:51 [inlined]
[11] macro expansion
@ ~/.julia/juliaup/julia-1.9.3+0.x64.linux.gnu/share/julia/stdlib/v1.9/Test/src/Test.jl:1498 [inlined]
[12] top-level scope
@ ~/FOSS/OMOPCDMCohortCreator.jl/test/runtests.jl:47
[13] include(fname::String)
@ Base.MainInclude ./client.jl:478
[14] top-level scope
@ none:6
[15] eval
@ ./boot.jl:370 [inlined]
[16] exec_options(opts::Base.JLOptions)
@ Base ./client.jl:280
[17] _start()
@ Base ./client.jl:522
Test Summary: | Pass Error Total Time
OMOPCDMCohortCreator | 43 1 44 10.3s
SQLite Helper Functions | 2 2 0.6s
SQLite Getter Functions | 33 1 34 9.3s
GetDatabasePersonIDs Tests | 1 1 0.6s
GetDatabaseYearRange Tests | 1 1 0.1s
GetPatientGender Tests | 1 1 0.5s
GetPatientRace Tests | 1 1 0.1s
GetPatientAgeGroup Tests | 2 2 0.9s
GetPatientVisits Tests | 2 2 0.2s
GetMostRecentConditions Tests | 2 2 0.3s
GetMostRecentVisit Tests | 2 2 0.6s
GetVisitConcept Tests | 1 1 0.2s
GetVisitCondition Tests | 2 2 0.1s
GetPatientEthnicity Tests | 1 1 0.1s
GetVisitDate Tests | 2 2 0.2s
GetDrugExposures Tests | 1 1 0.9s
GetDrugConceptIDs Tests | 1 1 0.2s
GetPatientGender multiple dispatch Tests | 1 1 0.3s
GetPatientRace multiple dispatch Tests | 1 1 0.1s
GetPatientAgeGroup multiple dispatch Tests | 1 1 0.4s
GetPatientVisits multiple dispatch Tests | 1 1 0.4s
GetMostRecentConditions multiple dispatch Tests | 1 1 0.2s
GetMostRecentVisit multiple dispatch Tests | 1 1 0.4s
GetVisitConcept multiple dispatch Tests | 1 1 0.2s
GetVisitCondition multiple dispatch Tests | 1 1 0.2s
GetPatientEthnicity multiple dispatch Tests | 1 1 0.1s
GetVisitDate multiple dispatch Tests | 2 2 0.1s
GetDrugExposures multiple dispatch Tests | 1 1 0.2s
GetDrugConceptIDs multiple dispatch Tests | 1 1 0.5s
GetCohortSubjects Tests | 1 1 1.1s
SQLite Filter Functions | 7 7 0.2s
SQLite Executors Functions | 1 1 0.2s
ERROR: LoadError: Some tests did not pass: 43 passed, 0 failed, 1 errored, 0 broken.
in expression starting at /home/thecedarprince/FOSS/OMOPCDMCohortCreator.jl/test/runtests.jl:46
ERROR: Package OMOPCDMCohortCreator errored during testing
The most important pieces it seems are:
Got exception outside of a @test
BoundsError: attempt to access 0-element Vector{Union{Missing, Float64}} at index [1:8]
and that it occurs around lines 412 and 407. Don't have time to take a look at the moment but this seems like where a problem is arising from.
Hm. Curious. I think it has something to do with the cohort table in the dataset. I know you were saying it passed locally on your computer but can you try deleting everything from your Cohort table within your dataset copy and re-run the test suite @Jay-sanjay ?
GOOD JOB!!! That was a lot of work and I am thrilled with how this turned out! :smile: Congratulations @Jay-sanjay -- very proud of the work here that you did!
Thanks for all the reviews and guidance till now @TheCedarPrince they mean a lot to me :)
This PR fixes #58
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