Changelog

Source: NEWS.md

hubValidations (development version)

• Added:
  • new vignette on how to create custom validation checks for hub validations (#121)
  • new section on how to manage additional dependencies required by custom validation functions (#22).

hubValidations 0.7.0

• Added function create_custom_check() for creating custom validation check function files from templates (#121).
• Fixed bug in check_tbl_values_required() causing required missing values to not be identified correctly when all output types were optional (#123)

hubValidations 0.6.2

• Fixed bug in check_tbl_col_types() where columns in model output data with more than one class were causing an EXEC error (#118). Thanks for the bug report @ruarai!

hubValidations 0.6.1

• Changed file name header colour in hub_validations object print() method to make more visible on lighter backgrounds.
• Soft deprecated file_modification_check argument "warn" option and replaced it with "failure" in validate_pr() function.

hubValidations 0.6.0

• To make clearer that all checks resulting in check_failure are required to pass for files to be considered valid, check_failure class objects are elevated to errors (#111). Also, to make it easier for users to identify errors from visually scanning the printed output, the following custom bullets have been assigned.
  • ✖ : check_failure class object. This indicates an error that does not impact the validation process.
  • ⓧ : check_error class object. This also indicates early termination of the validation process.
  • ☒ : check_exec_error class object. This indicates an error in the execution of a check function.
• hub_validations class object combine() method now ensures that check names are made unique across all hub_validations objects being combined.
• Additional improvements to hub_validations class object print() method.
  • Check results for each file validated are now split and printed under file name header.
  • The check name that can be used to access the check result from the hub_validations object is now included as the prefix to the check result message instead of the file name (#76).
• octolog dependency removed. This removes the annotation of validation results onto GitHub Action workflow logs (#113).

hubValidations 0.5.1

• Remove dependency on development version of arrow package and bump required version to 17.0.0.

hubValidations 0.5.0

This release introduces significant improvements in the performance of submission validation via the following changes:

• Add ability to sub-set expanded valid value grids by output type through output_type argument in expand_model_out_grid() (#98).
• Add ability to ignore the values of derived task IDs in expanded valid value grids through argument derived_task_ids in expand_model_out_grid().
• Use sub-setting and batching of model output data validation by output type in appropriate lower level checks and add ability to ignore derived task IDs in validate_model_data(), validate_submission() and validate_pr().

Both of these changes allow for the creation of smaller, more focused expanded valid value grids, significantly reducing pressure on memory when working with large, complex hub configs and making submission validation much more efficient.

Additional useful functionality:

• Add ability to subset by output type and ignore derived task IDs to submission_tmpl(). Ignoring derived task ids can be particularly useful to avoid creating templates with invalid derived task ID value combinations.
• Add new exported function match_tbl_to_model_task() that matches the rows in a tbl of model output data to a model task of a given round (as defined in tasks.json).

hubValidations 0.4.0

• Add new check_tbl_spl_compound_taskid_set() check function to validate_model_data() that ensures that sample compound task id sets for each modeling task match or are coarser than the expected set defined in tasks.json config.
• Add new get_tbl_compound_taskid_set() for detecting sample compound task ID set from submission data.
• Add argument compound_taskid_set to expand_model_out_grid() and submission_tmpl() that allows users to override the compound task ID set when creating sample indices in the output_type_id column of samples.

hubValidations 0.3.0

• Introduce an output_type_id_datatype argument to validate_pr(), validate_submission(), validate_model_data() and expand_model_out_grid() and set default value to "from_config". This default means the data type specified in the output_type_id_datatype property in tasks.json (introduced in schema version v3.0.1) is used to cast the hub level output_type_id column data type. If not set in the config, the functions fall back to "auto" which detects the simplest data type that can represent all output type id values across all output types and rounds. The argument also allows hub administrators to override this setting manually during validation.

hubValidations 0.2.0

• Move and rename the following hubData functions to hubValidations:
• hubData::expand_model_out_val_grid to expand_model_out_grid.
• hubData::create_model_out_submit_tmpl to submission_tmpl.

hubValidations 0.1.0

• Support validation of v3 schema sample submissions.

hubValidations 0.0.1

• Release stable 0.0.1 version
• Enforce minimum dependence on latest hubData (0.1.0) & hubAdmin (0.1.0). This allows for successful validation of submissions to hubs with multiple model tasks, where a given model task might contain non relevant task IDs and both required and optional properties have been set to null in tasks.json (#75). See the relevant section in hubDocs documentation for more details.
• Improve formatting of current time print in validate_submission_time() message by removing decimal seconds and including local time zone.

hubValidations 0.0.0.9008

• Added new articles on:
  • The structure of <hub_validations> class objects.
  • Validating Pull Requests on Github (for admins).
  • Validating Submissions locally (for teams).
• Added tables with details of individual checks performed by each high level validate_*() function to documentation.
• Fixed bug where check that values in value column are non-decreasing as output_type_ids increase for all unique task ID /output type value combinations for cdf and quantile output types was erroneously returning validation errors if the output_type_id column was not ordered. (Thanks @M-7th).

hubValidations 0.0.0.9007

• validate_pr() now has arguments for controlling modification/deletions check are performed on model output and model metadata files (#65).
  • file_modification_check, which controls whether modification/deletion checks are performed and what is returned if modifications/deletions detected.
  • allow_submit_window_mods, which controls whether modifications/deletions of model output files are allowed within their submission windows.

hubValidations 0.0.0.9006

• validate_pr() now checks for deletions of previously submitted model metadata files and modifications or deletions of previously submitted model output files, adding an <error/check_error> class object to the function output for each detected modified/deleted file (#43 & #44).

hubValidations 0.0.0.9005

• Improved handling of numeric output type IDs (including high precision floating points / values with trailing zeros), especially when overall hub output type ID column is character. This previously lead to a number of bugs and false validation failures (#58 & #54) which are addressed in this version.
• Bug fixes with respect to handling modelling tasks with no required task ID / output type combinations.
• Improved capture of error messages when check execution error occurs.

hubValidations 0.0.0.9004

This release contains a bug fix for reading in and validating CSV column types correctly. (#54)

hubValidations 0.0.0.9003

This release includes a number of bug fixes: - Deployment of custom/optional functions via validations.yml can now be accessed directly form pkg namespace, addressing bug which required pkg library to be loaded. (#51) - Use all.equal to check that sums of pmf probabilities equal 1. (#52)

hubValidations 0.0.0.9002

This release includes improvements designed after the first round of sandbox testing on setting up the CDC FluSight hub. Improvements include:

• Export parse_file_name function for parsing model output metadata from a model output file name.
• Issue more specific and informative messaging when check_tbl_values() check fails.
• Adding a verbose option to check_for_errors() function which prints the results of all checks in addition to the deafult overall result and subset of failed checks.

hubValidations 0.0.0.9001

• Release of first draft hubValidations package

hubValidations 0.0.0.9000

• Added a NEWS.md file to track changes to the package.