The MOLGENIS python REST Client allows you to retrieve, create, update and delete entities using python.

You can install the Python REST Client as a package with pip:

pip install molgenis-py-client

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

import molgenis.client
session = molgenis.client.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.client
session = molgenis.client.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 client, you can look at the examples on GitHub.

Methods

login

session.login(username,password)

Login to the MOLGENIS REST API

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.

get_by_id

session.get_by_id("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 Default
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 Default
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

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