R-api client

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()

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)

deleteList

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

Deletes a list of entities in an entityType.

Parameter	Description	Required
entity	The entityType name	yes
rows	List with ids of the rows	yes

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.

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