fhir_build_bundle {fhircrackr}

Build a FHIR bundle

Description

This function takes a table as produced by fhir_crack() with format="wide" and builds a fhir_bundle_xml object from it. It is primarily used to create transaction/batch bundles to POST back to a FHIR server. The column names of the table must represent the XPath expression of the respective element with indices for repeating items. A table like this is produced when FHIR resources have been cracked with fhir_crack() without assigning explicit column names in the fhir_design/fhir_table_description and the format has been set to "wide".

Usage

fhir_build_bundle(
  table,
  brackets,
  resource_type,
  bundle_type = "transaction",
  verbose = 1
)

## S4 method for signature 'data.frame'
fhir_build_bundle(
  table,
  brackets,
  resource_type,
  bundle_type = "transaction",
  verbose = 1
)

## S4 method for signature 'list'
fhir_build_bundle(table, brackets, bundle_type = "transaction", verbose = 1)

Arguments

table

A wide table as produced by fhir_crack(), possibly modified (see details) or a named list of wide tables, if different resource types have to be included in the same bundle. In this case the names of the list elements must correspond to the resource type represented in the table!

brackets

A character vector of length one. The brackets used for cracking.

resource_type

A character vector of length one or fhir_resource_type object indicating which resource type is represented in the table, if a single table is provided. This argument is ignored when table is a named list of tables.

bundle_type

A character vector of length one defining the bundle type. Will usually be either "transaction" (the default) or "batch".

verbose

An integer vector of length one. If 0, nothing is printed, if > 0 progress message is printed. Defaults to 1.

Details

The typical use case would look like this:

1. Download resources from a server with fhir_search()

2. Crack to wide format them with fhir_crack()

3. Do something to values (e.g. some kind of anonymization)

4. Translate the data back into FHIR resources with fhir_build_bundle()

5. Post the resources to a server

A FHIR bundle that can be POSTed to a server is usually of type transaction or batch. Each entry of these bundles consists of the resource itself as well as an instruction for the server of what to to with the resource. A very simple example looks like this:

<Bundle>
   <type value="transaction"/>
  <entry>
     <resource>
        <Patient>
           <id value="id1"/>
	       <address>
	          <city value="Amsterdam"/>
	          <country value="Netherlands"/>
	       </address>
	       <name>
	          <given value="Marie"/>
	       </name>
        </Patient>
    </resource>
    <request>
	   <method value="POST"/>
	   <url value="Patient"/>
    </request>
 </entry>
 <entry>
     <resource>
        <Patient>
           <id value="id2"/>
	       <address>
	          <city value="Paris"/>
	          <country value="France"/>
	       </address>
	       <name>
	          <given value="Anne"/>
	       </name>
        </Patient>
    </resource>
    <request>
	   <method value="POST"/>
	   <url value="Patient"/>
    </request>
 </entry>
</Bundle>

In this example the bundle contains two Patient resources that are sent to server with a POST. For more information the structure of transaction/batch bundles, please see the FHIR documentation at https://www.hl7.org/fhir/http.html and https://www.hl7.org/fhir/bundle.html.

In the table, each row corresponds to one resource that is created. To add the information for the request element of the bundle, this table has to be augmented with two columns named request.method and request.url, which contain the respective HTTP verb and URL for the resource. If these columns are not added to the table, fhir_build_bundle() still builds bundles from it, but those bundles will not be POSTable to a server. See examples.

Value

A fhir_bundle_xml object.

See Also

fhir_crack(),fhir_cast(), fhir_build_resource(), fhir_post()

Examples

#unserialize example
bundles <- fhir_unserialize(bundles = example_bundles1)

#crack fhir resources
table_desc_pat <- fhir_table_description(
    resource = "Patient",
    brackets = c("[", "]"),
    sep      = " ",
    format   = "wide"
)

df <- fhir_crack(bundles = bundles, design = table_desc_pat)

#add request info to table
request <- data.frame(
    request.method = c("POST", "PUT"),
    request.url    = c("Patient", "Patient/id3")
)

request_df <- cbind(df, request)

#build bundle
bundle <- fhir_build_bundle(table          = request_df,
                            brackets       = table_desc_pat@brackets,
                            resource_type  = "Patient",
                            bundle_type    = "transaction")

#print to console
cat(toString(bundle))