Common SQL Gen updates to support all studies

[comorbidity]

SQL gen count_encounter count_patient should have analogs for FHIR core table refs #100
#100

Import “study_prefix” into general ability to run counts generator
smart-on-fhir/cumulus-library-template#2

cumulus-library/cumulus_library/study_parser.py

Line 82 in 31a3888

def get_study_prefix(self) -> Optional[str]:

This is the most DRY violating thing currently in each study, because

• min_subjects is sometimes OK for studies that are small like Opioid but
• min_subjects is sometimes NEEDED for studies that are large like COVID

def write_view_sql(view_list_sql: List[str], filename="count.sql") -> None:

Typical naming scheme

STUDY_PREFIX + “count” + name of the source table + duration (optional)

Where duration is ONLY: {Month, Week, or None}

Should we ALWAYS default to creating TABLES rather than views? = YES 100%

[dogversioning]

Resolved via #109