Package 'omophub'

Description

Standalone wrapper for client$fhir$resolve(). See FhirResource for full parameter documentation.

Usage

fhir_resolve(client, ...)

Arguments

Value

A list with input and resolution.

See Also

FhirResource, fhir_resolve_batch(), fhir_resolve_codeable_concept()

Examples

## Not run: 
client <- OMOPHubClient$new(api_key = Sys.getenv("OMOPHUB_API_KEY"))
fhir_resolve(
  client,
  system = "http://snomed.info/sct",
  code = "44054006",
  resource_type = "Condition"
)

## End(Not run)

Description

Standalone wrapper for client$fhir$resolve_batch(). When as_tibble = TRUE, the result is a flat tibble suitable for dplyr/tidyr pipelines.

Usage

fhir_resolve_batch(client, ...)

Arguments

Value

See FhirResource$resolve_batch().

See Also

FhirResource, fhir_resolve(), fhir_resolve_codeable_concept()

Examples

## Not run: 
client <- OMOPHubClient$new(api_key = Sys.getenv("OMOPHUB_API_KEY"))
tbl <- fhir_resolve_batch(
  client,
  codings = list(
    list(system = "http://snomed.info/sct", code = "44054006"),
    list(system = "http://loinc.org", code = "2339-0")
  ),
  as_tibble = TRUE
)
dplyr::filter(tbl, status == "resolved")

## End(Not run)

Description

Standalone wrapper for client$fhir$resolve_codeable_concept().

Usage

fhir_resolve_codeable_concept(client, ...)

Arguments

Value

See FhirResource$resolve_codeable_concept().

See Also

FhirResource, fhir_resolve(), fhir_resolve_batch()

Examples

## Not run: 
client <- OMOPHubClient$new(api_key = Sys.getenv("OMOPHUB_API_KEY"))
fhir_resolve_codeable_concept(
  client,
  coding = list(
    list(system = "http://snomed.info/sct", code = "44054006"),
    list(system = "http://hl7.org/fhir/sid/icd-10-cm", code = "E11.9")
  ),
  resource_type = "Condition"
)

## End(Not run)

Description

Retrieves the OMOPHub API key from multiple sources in priority order:

1. Explicit argument

2. OMOPHUB_API_KEY environment variable

3. System keyring (if keyring package is installed)

Usage

get_api_key(key = NULL)

Arguments

Value

A character string containing the API key.

Examples

## Not run: 
# From environment variable
Sys.setenv(OMOPHUB_API_KEY = "your_api_key")
key <- get_api_key()

# Explicit key
key <- get_api_key("your_api_key")

## End(Not run)

Description

Checks whether an OMOPHub API key is available without throwing an error.

Usage

has_api_key()

Value

TRUE if an API key is available, FALSE otherwise.

Description

Convenience helper for constructing the OMOPHub FHIR Terminology Service base URL for a given FHIR version. Use it when configuring an external FHIR client library (httr2, fhircrackr, etc.) to talk to OMOPHub's FHIR endpoint directly.

Usage

omophub_fhir_url(version = c("r4", "r4b", "r5", "r6"))

Arguments

Value

A character scalar with the full FHIR base URL, e.g. "https://fhir.omophub.com/fhir/r4".

Examples

omophub_fhir_url()
omophub_fhir_url("r5")

## Not run: 
# Use with httr2 to call the $lookup operation directly
library(httr2)
req <- request(omophub_fhir_url()) |>
  req_url_path_append("CodeSystem/$lookup") |>
  req_url_query(
    system = "http://snomed.info/sct",
    code = "44054006"
  ) |>
  req_headers(Authorization = paste("Bearer", Sys.getenv("OMOPHUB_API_KEY")))
resp <- req_perform(req)

## End(Not run)

Description

R6 class for interacting with the OMOPHub vocabulary service. Provides access to OHDSI ATHENA standardized medical vocabularies.

Details

The client provides access to these resources:

• concepts: Concept lookup and batch operations

• search: Basic and advanced concept search

• vocabularies: Vocabulary listing and details

• domains: Domain listing and concept filtering

• hierarchy: Ancestor and descendant navigation

• relationships: Concept relationships

• mappings: Concept mappings between vocabularies

Value

A new OMOPHubClient object.

Active bindings

Methods

Public methods

• OMOPHubClient$new()

• OMOPHubClient$print()

• OMOPHubClient$clone()

Method new()

Create a new OMOPHub client.

Usage

OMOPHubClient$new(
  api_key = NULL,
  base_url = NULL,
  timeout = 30,
  max_retries = 3,
  vocab_version = NULL
)

Arguments

Method print()

Print client information.

Usage

OMOPHubClient$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

OMOPHubClient$clone(deep = FALSE)

Arguments

Examples

## Not run: 
# Create client (uses OMOPHUB_API_KEY env var)
client <- OMOPHubClient$new()

# Or with explicit API key
client <- OMOPHubClient$new(api_key = "your_api_key")

# Search for concepts
results <- client$search$basic("diabetes")

# Get a specific concept
concept <- client$concepts$get(201826)

# Use specific vocabulary version
client <- OMOPHubClient$new(vocab_version = "2025.1")

## End(Not run)

Description

Stores the OMOPHub API key in the specified location.

Usage

set_api_key(key, store = c("env", "keyring"))

Arguments

Value

Invisibly returns TRUE on success.

Examples

## Not run: 
# Store in environment (current session only)
set_api_key("your_api_key")

# Store securely in keyring (persistent)
set_api_key("your_api_key", store = "keyring")

## End(Not run)