sample.py

from notebook.base.handlers import IPythonHandler
import numpy as np
from .connection import openbis_connections

class SampleHandler(IPythonHandler):
    """Handle the requests for /openbis/sample/connection/permId"""

    def get_datasets(self, conn, permId):
        if not conn.is_session_active():
            try:
                conn.login()
            except Exception as exc:
                self.write({
                    "reason" : 'connection to {} could not be established: {}'.format(conn.name, exc)
                })

        sample = None
        try:
            sample = conn.openbis.get_sample(permId)
        except Exception as exc:
            self.set_status(404)
            self.write({
                "reason" : 'No such sample: {}'.format(permId)
            })
        if sample is None:
            return

        datasets = sample.get_datasets().df
        datasets.replace({np.nan:None}, inplace=True)  # replace NaN with None, otherwise we cannot convert it correctly
        return datasets.to_dict(orient='records')   # is too stupid to handle NaN


    def get(self, **params):
        """Handle a request to /openbis/sample/connection_name/permId
        download the data and return a message
        """
        try:
            conn = openbis_connections[params['connection_name']]
        except KeyError:
            self.write({
                "reason" : 'connection {} was not found'.format(
                    params['connection_name']
                )
            })
            return

        datasets = self.get_datasets(conn, params['permId'])
        if datasets is not None:
            self.set_status(200)
            self.write({
                "dataSets": datasets
            })