[WIP] Minimum Viable Product Draft 1

[annakrystalli]

This PR implements the first Minimum Viable Product of hubValidations functionality

General functionality consists of higher level functions containing multiple modular unit checks.

The higher level validate_* functions return objects (list) of class hub_validations. Unit check_*functions return the output ofcapture_check_cnd(), one of:

• <message/check_success> condition class object.
• <warning/check_failure> condition class object.
• <error/check_error> condition class object. Depending on whether validation has succeeded and whether the check has been designed to retunrn a warning or error on failure. Returned objects also inherit from subclass <hub_check>.

Functionality added:

• [x] validate_model_file() high level function running a number of unit checks on submitted model output data file.

  • check_file_exists(): checks that file exists at path specified by file_path. Returns check_error and triggers early return of caller fn.
  • check_file_name(): check that file name is correctly formatted and can be parsed for metadata. Returns check_error and triggers early return of caller fn.
  • check_file_location(): checks file is being submitted to correct location
  • check_valid_round_id(): check round_id is valid. Returns check_error and triggers early return of caller fn.
  • check_file_format(): checks that submitted file has file extension readable by hubValidations. Returns check_error and triggers early return of caller fn.

• [x] validate_model_data() high level function running a number of unit checks on submitted model output data file contents. #5

  • check_file_read(): checks that file can be read. Returns check_error and triggers early return of caller fn.
  • check_valid_round_id_col(): if applicable, checks that the round_id column can be parsed from the config file and/or is a valid column in tbl.
  • check_tbl_unique_round_id(): if applicable, checks that tbl contain single unique round ID in round id column. Returns check_error and triggers early return of caller fn.
  • check_tbl_colnames(): checks that tbl has expected columns according to config. Returns check_error and triggers early return of caller fn.
  • check_tbl_col_types(): checks that tbl column types match schema expected from config. #12
  • check_tbl_values(): checks that combinations of values in each row are valid combinations expected from config. #10
  • check_tbl_rows_unique(): checks that combinations of values in each row are unique.
  • check_tbl_values_required(): checks that all required combinations of values are present. #17, #10
  • check_tbl_value_col(): checks that value in the value column conform to expectations of type, min and max (where applicable) according to config. #19
  • check_tbl_value_col_ascending(): for cdf & quantile output types, checks that values in value column are non descending for each unique task ID value combination. #19
  • check_tbl_value_col_sum1(): for pmf output type, checks that values in value column sum to 1 for each unique task ID value combination. #19

Still to do:

• [x] validate_model_metadata(): high level function running a number of unit checks on model metadata file. (@elray1) #7
• [ ] Framework for running custom/optional validation functions/functions that require additional arguments.
• [ ] validate_submission_file(): Top level function that wraps validate_model_file(), validate_model_data() and validate_model_metadata().
• [ ] validate_pr() high level function for running validate_submission_file() on a file submitted through a PR. Functioniality to be largely based on https://github.com/covid19-forecast-hub-europe/HubValidations/blob/main/R/validate_pr.R