pycaravel: This module is designed to simplify continuous integration (CI) of data from multiple projects.

Note

Go to the end to download the full example code.

Validation¶

Credit: A Grigis

pycaravel is a Python package that enables you to apply validators. In this tutorial you will learn how to get and apply validators.

First checks¶

In order to test if pycaravel package is installed on your machine, you can check the package version.

import os
from pprint import pprint

import rlink
from rlink.validation import get_validators

import caravel
from caravel.validation import run_validation

print(caravel.__version__)
print(caravel.info())

Load the validators¶

First load the validators of the ‘rlink’ project that only check the MRI structure.

validators = get_validators(family="mri.structure")
print(validators)

Apply validators¶

Apply the loaded validators and generate a report.

datadir = "/neurospin/rlink/workspace/ci_toy/rlink-mri-upload"
projectdir = os.path.dirname(os.path.realpath(rlink.__file__))
parser = caravel.get_parser(
    project="rlink-mri", confdir=os.path.join(projectdir, "conf"),
    layoutdir=None)
parser.pickling_layout(
    bids_root=datadir, name="sourcedata", outdir=datadir)
parser.pickling_layout(
    bids_root=datadir, name="rawdata", outdir=datadir)
data = {
    "layoutdir": datadir,
    "confdir": os.path.join(projectdir, "conf"),
    "project": "rlink-mri"}
report = run_validation(data, validators=validators, logfile=None)
pprint(report)

Estimated memory usage: 0 MB

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