pybis.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-

"""
pybis.py

A class with methods for interacting with openBIS.

Created by Chandrasekhar Ramakrishnan on 2016-05-10.
Copyright (c) 2016 ETH Zuerich. All rights reserved.
"""

import os
import requests
from requests.packages.urllib3.exceptions import InsecureRequestWarning
requests.packages.urllib3.disable_warnings(InsecureRequestWarning)

import time
from datetime import datetime
import json
import re
from urllib.parse import urlparse

import pandas as pd
from pandas import DataFrame, Series

import threading
from threading import Thread
from queue import Queue
DROPBOX_PLUGIN = "jupyter-uploader-api"

def format_timestamp(ts):
    return datetime.fromtimestamp(round(ts/1000)).strftime('%Y-%m-%d %H:%M:%S')

class Openbis:
    """Interface for communicating with openBIS. A current version of openBIS is needed (at
    least version 16.05). 
    """

    def __init__(self, url='https://localhost:8443', verify_certificates=True, token=None):
        """Initialize an interface to openBIS with information necessary to connect to the server.
        :param host:
        """

        url_obj = urlparse(url)
        if  url_obj.netloc is None:
            raise ValueError("please provide the url in this format: https://openbis.host.ch:8443")

        self.url_obj = url_obj
        self.url     = url_obj.geturl()
        self.port    = url_obj.port
        self.hostname = url_obj.hostname
        self.as_v3 = '/openbis/openbis/rmi-application-server-v3.json'
        self.as_v1 = '/openbis/openbis/rmi-general-information-v1.json'
        self.reg_v1 = '/openbis/openbis/rmi-query-v1.json'
        self.verify_certificates = verify_certificates
        self.token = token
        self.datastores = []
        self.spaces = None
        self.dataset_types = None
        self.sample_types = None
        self.files_in_wsp = []
        self.token_path = None

        # use an existing token, if available
        if self.token is None:
            self.token = self._get_cached_token()


    def _get_cached_token(self):
        """Read the token from the cache, and set the token ivar to it, if there, otherwise None.
        If the token is not valid anymore, delete it. 
        """
        token_path = self.gen_token_path()
        if not os.path.exists(token_path):
            return None
        try:
            with open(token_path) as f:
                token = f.read()
                if not self.is_token_valid(token):
                    os.remove(token_path)
                    return None
                else:
                    return token
        except FileNotFoundError:
            return None


    def gen_token_path(self, parent_folder=None):
        """generates a path to the token file.
        The token is usually saved in a file called
        ~/.pybis/hostname.token
        """
        if parent_folder is None:
            # save token under ~/.pybis folder
            parent_folder = os.path.join(
                os.path.expanduser("~"),
                '.pybis'
            )
        path = os.path.join(parent_folder, self.hostname + '.token')
        return path


    def save_token(self, token=None, parent_folder=None):
        """ saves the session token to the disk, usually here: ~/.pybis/hostname.token
        """
        if token is None:
            token = self.token

        token_path = None;
        if parent_folder is None:
            token_path = self.gen_token_path()
        else:
            token_path = self.gen_token_path(parent_folder)

        # create the necessary directories, if they don't exist yet
        os.makedirs(os.path.dirname(token_path), exist_ok=True)
        with open(token_path, 'w') as f:
            f.write(token)
            self.token_path = token_path


    def delete_token(self, token_path=None):
        """ deletes a stored session token.
        """
        if token_path is None:
            token_path = self.token_path
        os.remove(token_path)


    def _post_request(self, resource, data):
        """ internal method, used to handle all post requests and serializing / deserializing
        data
        """
        resp = requests.post(
            self.url + resource, 
            json.dumps(data), 
            verify=self.verify_certificates
        )

        if resp.ok:
            data = resp.json()
            if 'error' in data:
                raise ValueError('an error has occured: ' + data['error']['message'] )
            elif 'result' in data:
                return data['result']
            else:
                raise ValueError('request did not return either result nor error')
        else:
            raise ValueError('general error while performing post request')


    def logout(self):
        """ Log out of openBIS. After that, the session token is no longer valid.
        """
        if self.token is None:
            return

        logout_request = {
            "method":"logout",
            "params":[self.token],
            "id":"1",
            "jsonrpc":"2.0"
        }
        resp = self._post_request(self.as_v3, logout_request)
        self.token = None
        self.token_path = None
        return resp


    def login(self, username=None, password=None, save_token=False):
        """Log into openBIS.
        Expects a username and a password and updates the token (session-ID).
        The token is then used for every request.
        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.
        """

        login_request = {
            "method":"login",
            "params":[username, password],
            "id":"1",
            "jsonrpc":"2.0"
        }
        result = self._post_request(self.as_v3, login_request)
        if result is None:
            raise ValueError("login to openBIS failed")
        else:
            self.token = result
            if save_token:
                self.save_token()
            return self.token


    def get_datastores(self):
        """ Get a list of all available datastores. Usually there is only one, but in some cases
        there might be more. If you upload a file, you need to specifiy the datastore you want
        the file uploaded to.
        """
        if len(self.datastores) == 0: