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

Just add

source("http://your.molgenis.url/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://your.molgenis.url/molgenis.R?molgenis-token=${molgenisToken}")))

Overview example

source("http://localhost:8080/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.

Parameter Description Required Default
entity The entity name yes
q Query string in rsql/fiql format (see below) No NULL
start The index of the thirst row to return No 0
num The maximum number of rows to return (max 10000) No 1000
attributes Vector of attributenames(columns) to return No All attributes
sortColumn attributeName of the column to sort on No NULL
sortOrder sort order, 'ASC' of 'DESC' No NULL

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

Operator Symbol
Logical AND ; or and
Logical OR , or or
Group ( and )
Equal to ==
Less then =lt= or <
Less then or equal to =le= or <=
Greater than =gt= or >
Greater tha or equal to =ge= or >=

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.

Parameter Description Required
entity The entity name of the entity to create yes
... Var arg list of attribute names and values yes

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.

Parameter Description Required
entity The entity name of the entity to create yes
rows data frame where each row represents an entity instance yes

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

Parameter Description Required
entity The entity name yes
id The id of the entity Yes
... Var arg list of attribute names and values yes

Example

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

delete

molgenis.delete(entity, id)

Deletes an entity.

Parameter Description Required
entity The entity name yes
id The id of the entity Yes

Example

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

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.

Parameter Description Required
entity The entity name yes
attribute The name of the attribute Yes

Example

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

results matching ""

    No results matching ""