openbis_urls: OpenBIS urls

In nbenn/infx: OpenBIS API Access to the InfectX Data Repository

OpenBIS urls

Description

The helper function api_url() is used to create urls to InfectX openBIS API endpoints and docs_link() generates latex links to documentation pages. Both functions support the following endpoints which are abbreviated as

• gis: \Sexpr[results=rd]{infx::docs_link("gis")}

• gics: \Sexpr[results=rd]{infx::docs_link("gics")}

• qas: \Sexpr[results=rd]{infx::docs_link("qas")}

• wis: \Sexpr[results=rd]{infx::docs_link("wis")}

• dsrg: \Sexpr[results=rd]{infx::docs_link("dsrg")}

• sas: \Sexpr[results=rd]{infx::docs_link("sas")}

• dsrs: \Sexpr[results=rd]{infx::docs_link("dsrs")}

Usage

api_url(api_endpoint = c("gis", "gics", "qas", "wis", "dsrg", "sas",
  "dsrs"), host_url = "https://infectx.biozentrum.unibas.ch",
  full_url = NULL, ...)

docs_link(api_endpoint = c("gis", "gics", "qas", "wis", "dsrg", "sas",
  "dsrs"), method_name = NULL, version = "13.04.0")

Arguments

api_endpoint	Abbreviated name of the API section (e.g. gis for IGeneralInformationService).
host_url	Host url.
full_url	Instead of constructing the API endpoint url, a string can be passed which will be returned again.
...	Further arguments are ignored.
method_name	Name of the method for which the link is created.
version	OpenBIS version number.

Details

If for some reason an url is desired from api_url() that cannot be constructed by pasting host_url and one of the hard-coded API endpoints together, this can be passed as full_url, which will simply be returned.

Value

A character vector of length 1.

See Also

Other utility functions: login_openbis, make_requests

Examples

# default endpoint is the GeneralInformationService interface
api_url()
# base url can be customized
api_url(host_url = "https://foobar.xyz")
# ScreeningApiServer interface endpoint
api_url("sas")
# manual url
api_url(full_url = "https://foobar.xyz/openbis/new-api-section-v1.json")

# link to GeneralInformationService interface docs
docs_link()
# add a method name (only to the link text)
docs_link(method_name = "foo_bar")
# link to ScreeningApiServer interface docs
docs_link("sas")
# link to most recent version of docs
docs_link("sas", version = "16.05.6")

nbenn/infx documentation built on May 20, 2022, 7:44 a.m.