The MOLGENIS python API client allows you to retrieve, create, update and delete entities using python.

Download molgenis.py from a molgenis server for instance using wget in the folder you want to run your molgenis api

wget https://molgenis.mydomain.example/molgenis.py

Now you can create a python script. To get started, you should import the python api, connect to a molgenis server and login:

import molgenis
session = molgenis.Session.("https://molgenis.mydomain.example/api/")
session.login("username","password")

Always put the import and molgenis.Session in your script to make the api work.

Overview example

import molgenis
session = molgenis.Session.("https://molgenis.mydomain.example/api/")
session.login("username","password")
my_table = session.get("package_entityName")
print(my_table)

To get a full overview of all functions in the python api, download the following zip: MolgenisPythonFunctions.zip

Methods

session.login(username,password)

Argument	Description	Required	Default
`username`	Username for a registered molgenis user	yes
`password`	Password for the user	yes

logout

session.logout()

Logout from the MOLGENIS REST API and destroy the session.

getById

session.getById("tableId", "rowId")

Retrieves a single entity row from an entity repository.

Argument	Description	Required	Default
`entity`	Fully qualified name of the entity	yes
`id`	The value for the idAttribute of the entity	yes
`attributes`	The list of attributes to retrieve	no	All attributes
`expand`	The attributes to expand	no	None

get

session.get("package_entityName")

Retrieves entities and returns the result in a dataframe.

Argument	Description	Required	Default
`entity`	Fully qualified name of the entity	yes
`q`	Query string in rsql/fiql format (see below)	no	None
`start`	The index of the first row to retrieve (zero indexed)	no	0
`num`	The maximum number of rows to return (max 10000)	no	100
`attributes`	The list of attributes to retrieve	no	All attributes
`sortColumn`	attributeName of the column to sort on	no	None
`sortOrder`	The order to sort in	no	None

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

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

add

session.add('Person', firstName='Jan', lastName='Klaassen')

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

Argument	Description	Required	Default
`entity`	Fully qualified name of the entity	yes
`files`	Dictionary containing file attribute values for the	no	Empty dictionary
	entity row. The dictionary should for each file
	attribute map the attribute name to a tuple
	containing the file name and an input stream.
`data`	Dictionary mapping attribute name to non-file	no	Empty dictionary
	attribute value for the entity row, gets merged
	with the kwargs argument
`**kwargs`	Keyword arguments get merged with the data argument	no

Examples

session.add('Person', {'firstName': 'Jan', 'lastName':'Klaassen'})
session.add('Plot', files={'image': ('expression.jpg', open('~/first-plot.jpg','rb')),
        'image2': ('expression-large.jpg', open('/Users/me/second-plot.jpg', 'rb'))},
        data={'name':'IBD-plot'})

update_one

session.update_one("entityType", "id", "attribute", "newValue")

Updates a value of a specified attribute in a specified row in a specified entityType.

Argument	Description	Required
`entity`	Fully qualified name of the entity	yes
`id`	The value for the idAttribute of the entity	yes
`attr`	Attribute to update	yes
`value`	New value of the attribute	yes

add_all

session.add_all(entity, entities)

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

Argument	Description	Required	Default
`entity`	Fully qualified name of the entity	yes
`entities`	List of dictionaries with the attributes of the entities	yes

Example

update = [{'id': '157', 'type': 'gnome', 'year': '1998'},
          {'id': '158', 'type': 'fairy', 'year': '1998'},
          {'id': '159', 'type': 'unicorn', 'year': '1998'}]


session.add_all("demo_sightings", update)

delete

session.delete(entity, id)

Deletes row based on its id.

Argument	Description	Required	Default
`entity`	Fully qualified name of the entity	yes
`id`	Id of the entity that should be deleted	yes

delete_list

session.delete_list(entity, entities)

Deletes a number of rows based on a list of id's.

Argument	Description	Required	Default
`entity`	Fully qualified name of the entity	yes
`entities`	List of id's of entities that should be deleted	yes

upload_zip

session.upload_zip("pathtozipfile")

This function uploads a zip file based on the EMX format.

Argument	Description	Required
`meta_data_zip`	A zip file containing an attribute, entities, packages file	yes
	(tsv/csv) to specify the meta data and optionally data
	defined in the meta data files

get_entity_meta_data

session.get_entity_meta_data(entity)

Retrieves the metadata for an entity repository.

Argument	Description	Required	Default
`entity`	Fully qualified name of the entity	yes

get_attribute_meta_data

session.get_attribute_meta_data(entity, attribute)

Retrieves the metadata for a single attribute of an entity repository.

Argument	Description	Required	Default
`entity`	Fully qualified name of the entity	yes
`attribute`	Name of the attribute	yes

Python api