Add Medication and Allergy CDA fields

[adamkells]

What does this do?

This PR adds the CDA fields of Medication and Allergy which were omitted from the original Clinical Documentation PR #47 . In particular it makes the following concrete changes:

• Renames get_concept_from_cda_value to get_medication_concept_from_cda_value.
• Adds equivalent functions for medication and allergies.
• Refactors the existing _extract_problems function to be more concise and less nested.
• Adds functions for _extract_medications and _extract_allergies.
• Adds an allergy code to the test_cda.xml file

[jenniferjiangkells]

Made some bug fixes and added tests. Of note:

• EntryRelationship can be list in allergy extraction
• overwrite wasn't working quite right when there are existing entries - fixed this and added tests
• Added a default allergy_type to AllergyConcept
• Some typos in add allergy entry function template

Let's merge it before I lose the will to live