Dedicated Metadata Class

[adamcantor22]

Is your feature request related to a problem? Please describe. Handling of metadata is inconsistent and redundant across MMEDS. There should be a single Metadata class that handles all functions relating to it.

Describe the solution you'd like A single python class that any MMEDS or QIIME metadata file can be imported into and modified. This should make heavy use of anapi, which was build exactly for this purpose. This should include such functions as: splitting/joining subject and specimen files, adding/removing metadata columns, and converting between used formats (MMEDS, QIIME, LEfSe).

Additional context Relates to the refactoring of util.py #433 and the reorganization of data and metadata #428

[adamcantor22]

Explicit datatype checks (e.g. datetime)

[adamcantor22]

validate.py and metadata_uploader.py should make heavy use of this class

[adamcantor22]

Functionality required in Metadata class:

• Search (e.g. "Find all cecum samples")
• Modify
  • Var names ("Age" -> "age")
  • Values ("N.A." -> "NA")
• Split vars (A.25.X -> [A, 25, X])
• Join vars^
• Match vars ("ID"_file1 ~ "SID"_file2)
• Add/drop vars
• Add/drop rows