Skip to content

FHIRCRACKR Release v1.0.1
Compare
Choose a tag to compare
@TPeschel TPeschel released this 18 Jun 08:52
· 269 commits to master since this release
v1.0.1
f0526e3

fhircrackr 1.0.1

The package is now rewritten using S4 classes. Almost all of the code written with fhircrackr < 1.0.1 will still work, though in a few cases the user will be prompted to change their code to the new syntax.

The most prominent change is how to create a design that tells fhir_crack() how to flatten HL7 FHIR® Resources. It should now be created using the functions fhir_table_description() and fhir_design(). fhir_crack() is now also able to create a single data.frame/data.table instead of a list of tables when just one resource type is extracted. Please see the documentation under ?fhir_table_description and ?fhir_design!

To get an overview about how the general workflow has changed, please have a look at the intro vignette (vignette("fhircrackr_intro", package="fhircrackr")).

There are a couple of new constructor functions for the newly defined classes which will not be listed here. Please have look at the package vignettes which go through them in detail.

Other new functions or behavior are listed in the following:

New functions

  • fhir_authenticate(): Set up authentication using OAuth2/OpenID Connect
  • fhir_current_request(): Get search request used in most recent call to fhir_search()or fhir_url()

New behavior

  • fhir_search() now allows for a search via POST via the argument body.

  • fhir_search() can now handle bearer token authentication via the argument token.

  • Argument save_to_file in fhir_search() now takes NULL or a string with a directory name and saves the bundles only if there is a specified directory. For backwards compatibility TRUE/FALSE in combination with directory are still allowed but discouraged with a warning.

  • Argument log_errors in fhir_search() now takes a string with a filename and writes an xml (no tables anymore) to the specified file. For backwards compatibility numbers are still allowed but discouraged with a warning.

  • New argument delay_between_bundles for fhir_search() allows to put a delay between the download of bundles (i.e. pages) in a bigger search request to prevent weak servers from choking.

  • The output of fhir_capability_statement() is slightly restructured: The names of the tables and their structure has changed.

  • The deprecated argument add_indices in fhir_crack() is now fully removed.

  • The most recently used FHIR search request is now implicitly saved whenever fhir_search() or fhir_url() is called. It can be accessed with the new function fhir_current_request().

  • The default value of rm_empty_cols is now FALSE

Assets 2
Loading