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Fix tests #60

Merged
merged 5 commits into from Jul 9, 2019
Merged

Fix tests #60

merged 5 commits into from Jul 9, 2019

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ibacher
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@ibacher ibacher commented Jul 9, 2019

A few fixes for the tests for this package:

  • Use in-memory SQLite
  • Ensure files are closed in test cases
  • MbedTLS was updated in a way that broke tests using HTTP. This is fixed using a hack.

@ibacher
Use in-memory SQLite for testing
ce53d7e
@ibacher
Close the zip file to ensure it can be cleanly deleted
add0e12
@ibacher
Hack to force loading of MbedTLS
154b411 
MbedTLS.jl (used by HTTP.jl) uses MbedTLS v2.16.0
LibCURL.jl (used by FTPClient.jl) uses MbedTLS v2.6.1

FTPClient.jl appears to be compatible with MbedTLS v2.16.0, but HTTP.jl
does not work properly with the older version.
@DilumAluthge
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@ibacher Tests are still failing, but I’ve unprotected master so you can merge if you want. We do need to get these tests passing though.

@DilumAluthge DilumAluthge mentioned this pull request Jul 9, 2019
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Examples are still failing with:

ERROR: LoadError: LoadError: UndefVarError: query not defined
Stacktrace:
 [1] top-level scope at /home/travis/build/bcbi/BioMedQuery.jl/examples/literate_src/1_pubmed_search_and_save.jl:82 [inlined]

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ibacher commented Jul 9, 2019

@DilumAluthge: Thanks. This is going to be a bit iterative, since I don't have a local instance of MySQL to test against...

@JuliaHealth JuliaHealth deleted a comment from codecov bot Jul 9, 2019
@JuliaHealth JuliaHealth deleted a comment from codecov bot Jul 9, 2019
@DilumAluthge
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No worries! That’s what Travis is for :)

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codecov bot commented Jul 9, 2019 •
edited

Codecov Report

Merging #60 into master will decrease coverage by 11.35%.
The diff coverage is 100%.

Impacted file tree graph

@@             Coverage Diff             @@
##           master      #60       +/-   ##
===========================================
- Coverage   78.58%   67.23%   -11.36%     
===========================================
  Files          14       14               
  Lines        1004     1004               
===========================================
- Hits          789      675      -114     
- Misses        215      329      +114
Impacted Files Coverage Δ
src/PubMed/pubmed_sql_utils.jl 58.57% <100%> (-3.58%) ⬇️
src/Processes/pubmed_mesh_to_umls_map.jl 0% <0%> (-89.4%) ⬇️
src/Processes/pubmed_occurrance_filtering.jl 0% <0%> (-80.96%) ⬇️
src/Processes/medline_load.jl 87.5% <0%> (-1.39%) ⬇️
src/PubMed/citation_manager.jl 85.05% <0%> (+2.29%) ⬆️

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@ibacher ibacher merged commit 22d22e1 into JuliaHealth:master Jul 9, 2019
@ibacher ibacher deleted the fix_tests branch July 9, 2019 19:29
@ibacher ibacher mentioned this pull request Jul 9, 2019
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Woo hoo!

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