From 763e54d3ec788f0bd973a22759317cbaf9dcbcb0 Mon Sep 17 00:00:00 2001
From: Chandrasekhar Ramakrishnan <chandrasekhar.ramakrishnan@id.ethz.ch>
Date: Tue, 10 May 2016 15:57:20 +0200
Subject: [PATCH] SSDM-3554: Templates for methods in the interface.
Implementation still needs to be filled out.
---
src/python/pybis/pybis.py | 51 +++++++++++++++++++++++++++++++++++++--
1 file changed, 49 insertions(+), 2 deletions(-)
diff --git a/src/python/pybis/pybis.py b/src/python/pybis/pybis.py
index c968523d073..b3a970a580b 100644
--- a/src/python/pybis/pybis.py
+++ b/src/python/pybis/pybis.py
@@ -16,7 +16,7 @@ import os
class OpenbisCredentials:
"""Credentials for communicating with openBIS."""
- def __init__(self, token = None, uname_and_pass = None):
+ def __init__(self, token=None, uname_and_pass=None):
"""A connection can be authenticated either by a token or a username and password combination
:param token: An authentication token for openBIS, can be None.
:param uname_and_pass: A tuple with username and password, in that order.
@@ -90,8 +90,55 @@ class Openbis:
def login(self):
"""Log into openBIS.
Expects credentials with username and password and updates the token on the credentials object.
+ Clients may want to store the credentials object in a credentials store after successful login.
Throw a ValueError with the error message if login failed.
"""
if not self.credentials.has_username_and_password:
raise ValueError('Cannot log into openBIS without a username and password')
- # TODO Implement the logic of this method.
+ # TODO Implement the logic of this method.
+
+ def is_token_valid(self):
+ """Check if the connection to openBIS is valid.
+ This method is useful to check if a token is still valid or if it has timed out, requiring the
+ user to login again.
+ :return: Return True if the token is valid, False if it is not valid.
+ """
+ if not self.credentials.has_token():
+ return False
+ # TODO Implement the logic of this method.
+
+ def get_samples(self, sample_identifiers):
+ """Retrieve metadata for the sample.
+ Get metadata for the sample and any directly connected parents of the sample to allow access
+ to the same information visible in the ELN UI. The metadata will be on the file system.
+ :param sample_identifiers: A list of sample identifiers to retrieve.
+ """
+ pass
+ # TODO Implement the logic of this method
+
+ def get_samples_with_data(self, sample_identifiers):
+ """Retrieve metadata for the sample, like get_sample_metadata, but retrieve any data sets as well,
+ like get_data_set.
+ :param sample_identifiers: A list of sample identifiers to retrieve.
+ """
+ pass
+ # TODO Implement the logic of this method
+
+ def get_data_sets(self, data_set_identifiers):
+ """Retrieve data set metadata and content.
+ The metadata will be on the file system. The file will also include the location of the data.
+ """
+ pass
+ # TODO Implement the logic of this method
+
+ def create_data_set_from_notebook(self, path_to_notebook, owner_identifier, paths_to_files,
+ parent_identifiers):
+ """Register a new data set with openBIS.
+ :param path_to_notebook: The path to the Jupyter notebook that created this data set
+ :param owner_identifier: The identifier of the sample that owns this data set.
+ :param paths_to_files: A list of paths to files that should be in the data set.
+ :param parent_identifiers: A list of parents for the data set.
+ :return:
+ """
+ pass
+ # TODO Implement the logic of this method
--
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