Errors in csv data found through DDL work

[gracebrownecodes]

Specific issues:

• pedsnet.v1.person.day_of_birth.type from numder -> number
• pedsnet.v2.vocabulary.vocabulary_concept_id from '' -> integer
• pedsnet.v1.indexes.idx_visit_person_id and ...idx_visit_concept_id replaced by ...idx_visit_person_date
• omop.v5.cohort_definition definitions field cohort_instantiation_date -> cohort_initiation_date
• omop.v5.concept definitions remove field concept_level
• omop.v5.fact_relationship schema field domain_concept_id split into ..._1 and ..._2
• omop.v5.constraints.primary_keys.xpk_cohort_attribute remove in favor of xpk_cohort_definition

Larger issues:

• Can the JSON object always adhere to the defined structure, even if the underlying lists are empty? (For example, can the pcornet.v3 json have schema.constraints.not_null and foreign_keys set to [] instead of none?)
• The omop.v4 json endpoint is not returning anything.
• Several pcornet.v1.schema.vital fields have integer types with a length attribute, which is choking the SQLAlchemy constructors... What is the intended meaning of this attribute? Should these be number types (with the length attribute moved to precision instead)?
• Downcase all object names in the pcornet models.
• Several i2b2.v1_7.schema fields share the integer with length problem described above.
• Is timestamp as used in i2b2.v1_7 significantly different from datetime elsewhere?

[bruth]

I updated the service to ensure the arrays are initialized: bbf73bb9b04

[bruth]

Which means the not_null and foreign_keys array will be empty arrays rather than nil.