Package manual

fetch_data_per_yaml(yaml_filepath, out_dir = "./out/"; use_axis_arrays::Bool = false, verbose = false, ...)

Refresh and load data products from the SCRC data registry. Checks the file hash for each data product and downloads anew any that are determined to be out-of-date.

Parameters

• yaml_filepath – the location of a .yaml file.
• out_dir – the local system directory where data will be stored.
• use_axis_arrays – convert the output to AxisArrays, where applicable.
• use_sql – load SQLite database and return connection.
• sql_file – (optional) SQL file for e.g. custom SQLite views, indexes, or whatever.
• db_path – (optional) specify the filepath of the database to use (or create.)
• force_db_refresh – overide filehash check on database insert.
• 'accesslogpath' – filepath of .yaml access log.
• verbose – set to true to show extra output in the console.

read_table(cn::SQLite.DB, data_product::String, [component::String]; data_type=nothing)

SQLite Data Registry helper function. Search and return [HDF5] table data as a DataFrame.

Parameters

• cn – SQLite.DB object.
• data_product – data product search string, e.g. "human/infection/SARS-CoV-2/%".
• component – as above, [required] search string for components names.

read_estimate(cn::SQLite.DB, data_product::String, [component::String]; data_type=nothing)

SQLite Data Registry helper function. Search TOML-based data resources stored in cn, a SQLite database created previously by a call to fetch_data_per_yaml.

Parameters

• cn – SQLite.DB object.
• data_product – data product search string, e.g. "human/infection/SARS-CoV-2/%".
• component – as above, optional search string for components names.
• data_type – (optional) specify to return an array of this type, instead of a DataFrame.

read_data_product_from_file(filepath; use_axis_arrays = false, verbose = false)

Read HDF5 or TOML file from local system.

Parameters

• filepath – the location of an HDF5 or TOML file.
• use_axis_arrays – convert the output to AxisArrays, where applicable.
• verbose – set to true to show extra output in the console.

register_github_model(model_config, scrc_access_tkn; ... )
register_github_model(model_name, model_version, model_repo, scrc_access_tkn; ... )

Register model as a code_repo_release in the SCRC data registry, from GitHub (default) or another source.

If used, the model_config file should include (at a minimum) the $model_name$, $model_version$ and $model_repo$ fields. Else these can be passed directly to the function.

Parameters

• model_config – path to the model config .yaml file.
• model_name – label for the model release.
• model_version – version number in the format 'n.n.n', e.g. $0.0.1$.
• model_repo – url of the model [e.g. GitHub] repo.
• scrc_access_tkn – access token (see https://data.scrc.uk/docs/.)
• model_description – (optional) description of the model.
• model_website – (optional) website, e.g. for an accompanying paper, blog, or model documentation.

register_model_run(model_config, code_repo_release_uri, model_run_description, scrc_access_tkn)

Upload model run to the $code_run$ endpoint of the SCRC Data Registry.

Parameters

• model_config – path to the model config .yaml file.
• submission_script_text – e.g. 'julia my/julia/code.jl'.
• code_repo_release_uri – Data Registry uri of the model $code_repo_release$, i.e. the model code such as an (already registered) GitHub repo.
• model_run_description – description of the model run.
• scrc_access_tkn – access token (see https://data.scrc.uk/docs/.)

register_text_file(text, code_repo_release_uri, model_run_description, scrc_access_tkn, search=true)

Post an entry to the $text_file$ endpoint of the SCRC Data Registry.

Note that according to the docs, "".

Parameters

• text – text file contents.
• description – object description.
• scrc_access_tkn – access token (see https://data.scrc.uk/docs/.)
• search – (optional, default=true) check for existing entry by path and file hash.
• hash_val – (optional) specify the file hash, else it is computed based on text.