The MOLGENIS R API client allows you to retrieve, create, update and delete entities from within the R environment.

Just add

source("http://molgenis.mydomain.example/molgenis.R")

at the top of your script and you can connect to a MOLGENIS server. Typically the first thing you do is login and the last thing is logout.

NOTE: For https connections use

eval(expr = parse(text = getURL("https://molgenis.mydomain.example/molgenis.R?molgenis-token=${molgenisToken}")))

NOTE: The MOLGENIS R-api client supports up to R-version 3.2.x

Overview example

source("http://molgenis.mydomain.example/molgenis.R")


molgenis.login("admin", "admin")

df <- molgenis.get("celiacsprue", 
                   q = "celiac_weight>80 and celiac_height>180",
                   num = 1000,
                   attributes = c("celiac_weight", "celiac_height", "celiac_gender"))

plot(df$Celiac_Height ~ df$Celiac_Weight, col=df$Celiac_Gender)

molgenis.logout()

Methods

login

molgenis.login(username,password)

Login to the MOLGENIS REST API

logout

molgenis.logout()

Logout from the MOLGENIS REST API and destroy the session.

get

molgenis.get (entity, q = NULL, start = 0, num = 1000, attributes = NULL)

Retrieves entities and returns the result in a dataframe.

Supported RSQL/FIQL query operators (see https://github.com/jirutka/rsql-parser)

Argument can be a single value, or multiple values in parenthesis separated by comma. Value that doesn’t contain any reserved character or a white space can be unquoted, other arguments must be enclosed in single or double quotes.

Examples

molgenis.get("celiacsprue")
molgenis.get("celiacsprue", num = 100000, start = 1000)
molgenis.get("celiacsprue", attributes = c("Individual", "celiac_gender"))
molgenis.get("celiacsprue", q = "(celiac_weight>=80 and celiac_height<180) or (celiac_gender==Female)")
molgenis.get("celiacsprue", q = "(celiac_weight>=80;celiac_height<180),(celiac_gender==Female)")

add

molgenis.add(entity, ...)

Creates a new instance of an entity (i.e. a new row of the entity data table) and returns the id.

Example

id <- molgenis.add(entity = "Person", firstName = "Piet", lastName = "Paulusma")

addAll

molgenis.addAll(entity, rows)

Creates new instances of an entity (i.e. adds new rows to the entity data table) and returns the ids.

Example

firstName <- c("Piet", "Paulusma")
lastName <- c("Klaas", "de Vries")
df <- data.frame(firstName, lastName)

molgenis.addAll("Person", df)

update

molgenis.update(entity, id, ...)

Updates un existing entity

Example

molgenis.update(entity = "Person", id = 8, firstName = "Pietje", lastName = "Paulusma")

delete

molgenis.delete(entity, id)

Deletes an entity.

Example

molgenis.delete(entity = "Person", id = 8)

deleteList

molgenis.deleteList(entity, c("id1", "id2"))

Deletes a list of entities in an entityType.

Example

molgenis.deleteList(entity = "Person", rows = c("1", "2", "3"))

getEntityMetaData

molgenis.getEntityMetaData(entity)

Gets the entity metadata as list.

Example

meta <- molgenis.getEntityMetaData("celiacsprue")
meta$label

getAttributeMetaData

molgenis.getAttributeMetaData(entity, attribute)

Gets attribute metadata as list.

Example

attr <- molgenis.getAttributeMetaData(entity = "celiacsprue", attribute = "celiac_gender")
attr$fieldType