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X-DataInitiative / SCALPEL-Extraction

SCALPEL extraction library to fetch concepts from flattened SNDS
BSD 3-Clause "New" or "Revised" License
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Cnam-452: ExtractorCodes #250

Closed ysebiat closed 4 years ago

ysebiat commented 4 years ago

Refactoring the Extractor trait that aims to add coherence and reduce the redundancy of some codes parts. Here are the changes:

  1. Extractor trait has now a new getCodesmethod. It returns a ExtractorCodestype.
  2. An ExtractorCodes is a trait that allows to pass a code that are more complex than a simple Set. This allows to have complex codes such as DrugConfig and NgapConfig.
  3. A BasicExtractor is a new trait. It is intended for Extractorsthat are simple and that uses EventRowExtractor trait to get all the information from the Row to build an Event.
  4. Every source, has now an implementation of EventRowExtractorimplementation. This allows to unify the extraction of information of Event such patientID and groupID.
codecov[bot] commented 4 years ago

Codecov Report

Merging #250 into develop will decrease coverage by 0.09%. The diff coverage is 94.76%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #250      +/-   ##
===========================================
- Coverage    93.40%   93.30%   -0.10%     
===========================================
  Files          204      218      +14     
  Lines         2503     2526      +23     
  Branches        75       72       -3     
===========================================
+ Hits          2338     2357      +19     
- Misses         165      169       +4
Impacted Files Coverage Δ
...ytechnique/cmap/cnam/etl/config/ConfigLoader.scala 100.00% <ø> (ø)
...olytechnique/cmap/cnam/etl/events/MedicalAct.scala 100.00% <ø> (ø)
...chnique/cmap/cnam/etl/extractors/ColumnNames.scala 100.00% <ø> (ø)
...etl/extractors/events/acts/MedicalActsConfig.scala 100.00% <ø> (ø)
.../extractors/events/diagnoses/DiagnosesConfig.scala 100.00% <ø> (ø)
...gs/classification/PharmacologicalClassConfig.scala 100.00% <ø> (ø)
...rugs/classification/families/Antidepresseurs.scala 100.00% <ø> (ø)
...drugs/classification/families/Antiepileptics.scala 100.00% <ø> (ø)
...gs/classification/families/Antihypertenseurs.scala 100.00% <ø> (ø)
...events/drugs/classification/families/Cardiac.scala 100.00% <ø> (ø)
... and 144 more

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