Description

Addresses #112

Changes

• Add fhir.resources as a dependency
• Removed fhir_resources and replaced usage with fhir.resource library
• Removed CcdData, CdsFhirData, Concept and replaced with native use of FHIR resources and usages in several modules:
  • CdaAnnotator
  • data_generators
  • io.connectors
  • use_cases
• Renamed Document.hl7 -> Document.fhir for more accurate description and removed Document.concepts as no longer needed
• HL7Data -> FhirData along with updated methods to access bundle and cds FHIR resources.
• Use setters and getters for properties in Document
• CDS prefetch data generator is closer to specification ({prefetch_key_name: Resource}) instead of everything in one Bundle and uses a Prefetch pydantic model for validation
• Updated and moved SpacyNLP._add_concepts_to_hc_doc-> Document.update_problem_list_from_nlp() for better separation of concerns and usage
• Added a fhir module with helper functions that make it easier to create and access data in FHIR resources
• Added a .model_dump() method to CDSRequest that serializes bytes and datetime objects in FHIR resources. This is a workaround as it's better to use .model_dump_json() for serialization, but there is an issue in Pydantic v2 where timezones don't get dumped correctly. Timezone information is required for FHIR.
• Updated tests and docs