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Bugfix/kbdev 1047 civic updated evidences last #155

Merged
merged 27 commits into from
Jun 3, 2024
Merged

Bugfix/kbdev 1047 civic updated evidences last #155

merged 27 commits into from
Jun 3, 2024

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mathieulemieux
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@mathieulemieux mathieulemieux commented May 27, 2024 •
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Here is a major refactoring of the CIViC loader:

  • Already existing GraphKB statements are now updated again, by default
  • A noUpdate flag can be used at the command line to avoid update/delete operations when needed
  • A bug in the Molecular Profile parser has been fixed

Also:

  • Code has been splitted up in smaller functions and more files for clarity
  • Comments and jsdocs has been added to functions
  • Some test has been added or updated
  • Logging has been improved

@mathieulemieux
Fix MolecularProfile._disambiguate()
9a5d41f
@mathieulemieux
Add processMolecularProfile() for MP cache management
09f36a0
@mathieulemieux
Add variants required in EvidenceItems specs
71bcabf
@mathieulemieux
Pubmed caching from module.exports
3c5d3df
@mathieulemieux
Better jsdocs and comments in publications.js
904ee7c
@mathieulemieux
Minor changes to getRelevance()
978f9f0
@mathieulemieux
Add support for cache inside processVariantRecord()
062a822
@mathieulemieux
Comments and exports in variant.js
974a6ed
@mathieulemieux
Refactoring therapies in seperated file
9e9c533
@mathieulemieux
Minor test updates
e26b8aa
@mathieulemieux
Moving civic tests in own directory
bb39bb6
@mathieulemieux
Moving EvidenceLevels in seperated file
44f20a9
@mathieulemieux
Moving Disease in seperated file
d55fe82
@mathieulemieux
Add comments in graphkb.js
7d2f189
@mathieulemieux
Remove unused variables
69552cf
@mathieulemieux
Add EvidenceItem file in preperation for major civic upload function …
3e66512 
…refactoring
@mathieulemieux
Add Statement file and tests in preperation for major civic upload fu…
a767a22 
…nction refactoring
@mathieulemieux
remove debugger
3561dac
@mathieulemieux
Add noUpdate flag to civic parser
35ac6b7
@mathieulemieux
Refactoring main loop in civic upload
ff73e99
@mathieulemieux
Linting and removing extra
84615a5
@mathieulemieux mathieulemieux added the CIViC To do with the CIViC data loader label May 27, 2024
@mathieulemieux mathieulemieux self-assigned this May 27, 2024
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@mathieulemieux
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As of this morning while running the loader on dev:

Loader log:
log_dev_May29.log

Error log:
errorLog-1717001282973-civic.json

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New logs after new handling of cases to review:

log_dev_3june.log
errorLog-1717434206192-civic.json

@mathieulemieux mathieulemieux merged commit 26a7a56 into develop Jun 3, 2024
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github-actions bot commented Jun 3, 2024

Unit Test Results

0 files  ±0  0 suites  ±0   0s ⏱️ ±0s
0 tests ±0  0 ✔️ ±0  0 💤 ±0  0 ❌ ±0 

Results for commit 26a7a56. ± Comparison against base commit 1710f45.

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Here is a small doc on how the loader works:

gkb_loader_civic_doc_v2.pdf

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Reviewers

@elewis2 elewis2 elewis2 approved these changes

@sshugsc sshugsc Awaiting requested review from sshugsc

@cgrisdale cgrisdale Awaiting requested review from cgrisdale

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@mathieulemieux mathieulemieux

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