molgenis-py-bbmri-eric 1.0.3

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molgenis-py-bbmri-eric

MOLGENIS Python tooling for BBMRI-ERIC.

Description

This library contains tools for the MOLGENIS BBMRI-ERIC Directory that help with staging and publishing the data of the national nodes. Staging is the process of copying data from a national node's external server (for example BBMRI-NL) to the staging area on the ERIC directory. Not all national nodes have external servers; these do not need to be staged. Publishing is the process of copying and combining the data from the staging areas to the public combined tables of the directory.

Usage

These tools can be used as a library in a script or as a command line tool. In both cases, start by installing the library with pip install molgenis-py-bbmri-eric.

On the command line

The command line tool is called eric. Here are some usage examples:

Stage all external nodes:

eric stage all

Publish nodes UK and NL:

eric publish uk nl

Use another server as the directory:

eric stage be --target <URL_TO_DIRECTORY>

Please read the tool's help page (eric -h) for more information.

In a script

from molgenis.bbmri_eric.bbmri_client import EricSession
from molgenis.bbmri_eric.eric import Eric

# First, initialise an EricSession (an extension of the molgenis-py-client Session)
session = EricSession(url="<DIRECTORY_URL>")
session.login("<USERNAME>", "<PASSWORD>")

# Get the nodes you want to work with
nodes_to_stage = session.get_external_nodes(["NL", "BE"])
nodes_to_publish = session.get_nodes() # all nodes

# Create an Eric instance and use that to perform the desired actions
eric = Eric(session)
staging_report = eric.stage_external_nodes(nodes_to_stage)
publishing_report = eric.publish_nodes(nodes_to_publish)

if publishing_report.has_errors():
    raise ValueError("Some nodes did not publish correctly")

If you want to use the data of a node for another purpose, you can use the EricSession and ExternalServerSession to retrieve these.

from molgenis.bbmri_eric.bbmri_client import EricSession, ExternalServerSession
from molgenis.bbmri_eric.model import NodeData

# Get the staging and published data of NL from the directory
session = EricSession(url="<DIRECTORY_URL")
nl = session.get_nodes(["NL"])
nl_staging_data: NodeData = session.get_staging_node_data(nl)
nl_published_data: NodeData = session.get_published_node_data(nl)

# Get the data from the external server of NL
external_session = ExternalServerSession(node=nl)
nl_external_data: NodeData = external_session.get_node_data()

# Now you can use the NodeData objects as you wish
for person in nl_external_data.persons.rows:
    print(person)

For developers

This project uses pre-commit and pipenv for the development workflow.

Install pre-commit and pipenv if you haven't already:

pip install pre-commit
pip install pipenv

Install the git commit hooks:

pre-commit install

Create an environment and install the package including all (dev) dependencies:

pipenv install

Enter the environment:

pipenv shell

Build and run the tests:

tox

The package's command-line entry point is already installed

eric -h

Note

This project has been set up using PyScaffold 4.0.2. For details and usage information on PyScaffold see https://pyscaffold.org/.