Package hierarchies should be normalized

[sheridancbio]

After a new shared module (common), it is clear that there is discord between the package naming hierarchies among the various pipelines in this repo. This is not only confusing ... but it complicates component scanning among modules.

For example ... a cvr fetcher package example: cvr/src/main/java/org/cbioportal/cmo/pipelines/cvr ... and a darwin fetcher package example: darwin/src/main/java/org/mskcc/cmo/ks/darwin/pipeline ... and a crdb fetcher package example: crdb/src/main/java/org/mskcc/cmo/ks/crdb/pipeline ... and a redcap pipeline example: redcap/redcap_pipeline/src/main/java/org/mskcc/cmo/ks/redcap/pipeline ... and a gene pipeline example: gene/src/main/java/org/mskcc/cmo/ks/gene

... and the new common example: common/src/main/java/org/cbioportal/cmo/pipelines/common

Two main questions:

• what is our organizational root (org.cbioportal ... or org.mskcc ??
• how should individual modules be separated into subpackages (naming scheme)?

When we fix the packages: change this: @ComponentScan(basePackages = {"org.mskcc.cmo.ks.darwin.pipeline", "org.cbioportal.cmo.pipelines.common"}) in darwin/src/main/java/org/mskcc/cmo/ks/darwin/pipeline/DarwinEmailTasklet.java.

[ao508]

@sheridancbio the package naming convention should follow org/mskcc/cmo/ks/.., so the cvr common modules should be refactored to match this convention