Provide hook to optimize cohort SQL construction

[anthonysena]

The Strategus analysis specification embeds Circe JSON for each cohort definition. As an example, the cohortDefinition element contains the Circe JSON:

Strategus/inst/testdata/cdmModulesAnalysisSpecifications.json

Lines 4 to 9 in 612859f

	"cohortDefinitions": [
	{
	"cohortId": 1,
	"cohortName": "Celecoxib",
	"cohortDefinition": "{\r\n\t\"cdmVersionRange\" : \">=5.0.0\",\r\n\t\"PrimaryCriteria\" : {\r\n\t\t\"CriteriaList\" : [\r\n\t\t\t{\r\n\t\t\t\t\"DrugEra\" : {\r\n\t\t\t\t\t\"CodesetId\" : 0\r\n\t\t\t\t}\r\n\t\t\t}\r\n\t\t],\r\n\t\t\"ObservationWindow\" : {\r\n\t\t\t\"PriorDays\" : 0,\r\n\t\t\t\"PostDays\" : 0\r\n\t\t},\r\n\t\t\"PrimaryCriteriaLimit\" : {\r\n\t\t\t\"Type\" : \"First\"\r\n\t\t}\r\n\t},\r\n\t\"ConceptSets\" : [\r\n\t\t{\r\n\t\t\t\"id\" : 0,\r\n\t\t\t\"name\" : \"Celecoxib\",\r\n\t\t\t\"expression\" : {\r\n\t\t\t\t\"items\" : [\r\n\t\t\t\t\t{\r\n\t\t\t\t\t\t\"concept\" : {\r\n\t\t\t\t\t\t\t\"CONCEPT_ID\" : 1118084,\r\n\t\t\t\t\t\t\t\"CONCEPT_NAME\" : \"celecoxib\",\r\n\t\t\t\t\t\t\t\"STANDARD_CONCEPT\" : \"S\",\r\n\t\t\t\t\t\t\t\"STANDARD_CONCEPT_CAPTION\" : \"Standard\",\r\n\t\t\t\t\t\t\t\"INVALID_REASON\" : \"V\",\r\n\t\t\t\t\t\t\t\"INVALID_REASON_CAPTION\" : \"Valid\",\r\n\t\t\t\t\t\t\t\"CONCEPT_CODE\" : \"140587\",\r\n\t\t\t\t\t\t\t\"DOMAIN_ID\" : \"Drug\",\r\n\t\t\t\t\t\t\t\"VOCABULARY_ID\" : \"RxNorm\",\r\n\t\t\t\t\t\t\t\"CONCEPT_CLASS_ID\" : \"Ingredient\"\r\n\t\t\t\t\t\t},\r\n\t\t\t\t\t\t\"isExcluded\" : false,\r\n\t\t\t\t\t\t\"includeDescendants\" : false,\r\n\t\t\t\t\t\t\"includeMapped\" : false\r\n\t\t\t\t\t}\r\n\t\t\t\t]\r\n\t\t\t}\r\n\t\t}\r\n\t],\r\n\t\"QualifiedLimit\" : {\r\n\t\t\"Type\" : \"First\"\r\n\t},\r\n\t\"ExpressionLimit\" : {\r\n\t\t\"Type\" : \"First\"\r\n\t},\r\n\t\"InclusionRules\" : [],\r\n\t\"EndStrategy\" : {\r\n\t\t\"CustomEra\" : {\r\n\t\t\t\"DrugCodesetId\" : 0,\r\n\t\t\t\"GapDays\" : 30,\r\n\t\t\t\"Offset\" : 0\r\n\t\t}\r\n\t},\r\n\t\"CensoringCriteria\" : [],\r\n\t\"CollapseSettings\" : {\r\n\t\t\"CollapseType\" : \"ERA\",\r\n\t\t\"EraPad\" : 0\r\n\t},\r\n\t\"CensorWindow\" : {}\r\n}"
	},

The StrategusModule base class then iterates over each cohort definition to translate the Circe JSON to a SQL statement using the CirceR package (ref) to build out the cohortDefinitionSet. The cohortDefinitionSet is then used by CohortGenerator to construct the cohorts in the study. Other modules may also use the cohortDefinitionSet which is why this code is located in the StrategusModule base class.

Some OHDSI network sites have optimizations for the Circe-generated SQL to allow it to run performantly at their site. So, we'd like to provide a way for sites to hook into the cohortDefinitionSet construction process to apply their SQL optimization. At the moment this requires a user to override the CohortGeneratorModule class which is not ideal.