CNAM-294-separate-source-filtering

[danielpes]

• Added the SourceSanitizer trait, which adds the sanitize method (DF -> DF). By default it does nothing to the data.
• All source objects now extend SourceManager, which mixes both SourceReader and SourceSanitizer in.
• All source objects that contains a filter, now perform the filter in the overriden sanitize method. Their read methods now only perform the read operation.
• Changed the "Sources" class and object to reflect those changes (and to add some refactoring)
• The study-specific main classes now perform read and sanitize to the sources before passing them to the extractors
• This PR doesn't add reporting between reading and sanitizing, this is for a future PR

[codecov[bot]]

Codecov Report

Merging #125 into master will increase coverage by 0.05%. The diff coverage is 90.47%.

@@            Coverage Diff             @@
##           master     #125      +/-   ##
==========================================
+ Coverage   86.45%   86.51%   +0.05%     
==========================================
  Files         107      108       +1     
  Lines        1654     1668      +14     
  Branches       51       32      -19     
==========================================
+ Hits         1430     1443      +13     
- Misses        224      225       +1

Impacted Files	Coverage Δ
...m/etl/extractors/molecules/MoleculePurchases.scala	100% <ø> (ø)	:arrow_up:
...map/cnam/etl/extractors/drugs/DrugsExtractor.scala	100% <ø> (ø)	:arrow_up:
...technique/cmap/cnam/etl/sources/SourceReader.scala	100% <ø> (ø)	:arrow_up:
.../cnam/etl/extractors/tracklosses/Tracklosses.scala	100% <ø> (ø)	:arrow_up:
...map/cnam/study/pioglitazone/PioglitazoneMain.scala	0% <0%> (ø)	:arrow_up:
...p/cnam/study/rosiglitazone/RosiglitazoneMain.scala	0% <0%> (ø)	:arrow_up:
...ue/cmap/cnam/etl/extractors/acts/MedicalActs.scala	100% <100%> (ø)	:arrow_up:
.../polytechnique/cmap/cnam/study/fall/FallMain.scala	90.56% <100%> (-0.09%)	:arrow_down:
...lytechnique/cmap/cnam/etl/sources/DcirSource.scala	100% <100%> (ø)
...echnique/cmap/cnam/etl/sources/DosagesSource.scala	100% <100%> (ø)
... and 11 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 6685ceb...59f8e8d. Read the comment docs.

[ysebiat]

Ready to be merged for me.