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236 lines
8.1 KiB
Python
236 lines
8.1 KiB
Python
"""
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Data Transport, The Phi Technology LLC
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Steve L. Nyemba, steve@the-phi.com
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This library is designed to serve as a wrapper to a set of supported data stores :
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- couchdb
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- mongodb
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- Files (character delimited)
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- Queues (RabbmitMq)
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- Session (Flask)
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- s3
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- sqlite
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The supported operations are read/write and providing meta data to the calling code
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We separated reads from writes to mitigate accidents associated with writes.
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Source Code is available under MIT License:
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https://healthcareio.the-phi.com/data-transport
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https://hiplab.mc.vanderbilt.edu/git/hiplab/data-transport
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"""
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import numpy as np
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#from transport import sql, nosql, cloud, other, warehouse
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from transport import sql
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try:
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from transport import nosql
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except Exception as e:
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nosql = {}
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try:
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from transport import cloud
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except Exception as e:
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cloud = {}
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try:
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from transport import warehouse
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except Exception as e:
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warehouse = {}
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try:
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from transport import other
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except Exception as e:
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other = {}
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import pandas as pd
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import json
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import os
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from info import __version__,__author__,__email__,__license__,__app_name__,__whatsnew__,__edition__
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from transport.iowrapper import IWriter, IReader, IETL
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from transport.plugins import PluginLoader
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from transport import providers
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import copy
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from transport import registry
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from transport.plugins import Plugin
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PROVIDERS = {}
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def init():
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global PROVIDERS
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for _module in [cloud,sql,nosql,other,warehouse] :
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for _provider_name in dir(_module) :
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if _provider_name.startswith('__') or _provider_name == 'common' or type(_module) in [None,str,dict]:
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continue
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PROVIDERS[_provider_name] = {'module':getattr(_module,_provider_name),'type':_module.__name__}
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#
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# loading the registry
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if not registry.isloaded() :
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registry.load()
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# def _getauthfile (path) :
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# f = open(path)
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# _object = json.loads(f.read())
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# f.close()
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# return _object
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def instance (**_args):
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"""
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This function returns an object of to read or write from a supported database provider/vendor
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@provider provider
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@context read/write (default is read)
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@auth_file: Optional if the database information provided is in a file. Useful for not sharing passwords
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kwargs These are arguments that are provider/vendor specific
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"""
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global PROVIDERS
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if 'auth_file' in _args:
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if os.path.exists(_args['auth_file']) :
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#
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# @TODO: add encryption module and decryption to enable this to be secure
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#
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f = open(_args['auth_file'])
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#_args = dict (_args,** json.loads(f.read()) )
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#
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# we overrite file parameters with arguments passed
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_args = dict (json.loads(f.read()),**_args )
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f.close()
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else:
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filename = _args['auth_file']
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raise Exception(f" {filename} was not found or is invalid")
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if 'provider' not in _args and 'auth_file' not in _args :
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if not registry.isloaded () :
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if ('path' in _args and registry.exists(_args['path'] )) or registry.exists():
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registry.load() if 'path' not in _args else registry.load(_args['path'])
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_info = {}
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if 'label' in _args and registry.isloaded():
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_info = registry.get(_args['label'])
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else:
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_info = registry.get()
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if _info :
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_args = dict(_info,**_args) #-- we can override the registry parameters with our own arguments
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if 'provider' in _args and _args['provider'] in PROVIDERS :
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_info = PROVIDERS[_args['provider']]
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_module = _info['module']
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if 'context' in _args :
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_context = _args['context']
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else:
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_context = 'read'
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_pointer = getattr(_module,'Reader') if _context == 'read' else getattr(_module,'Writer')
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_agent = _pointer (**_args)
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#
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loader = None
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#
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# @TODO:
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# define a logger object here that will used by the wrapper
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# this would allow us to know what the data-transport is doing and where/how it fails
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#
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# if 'plugins' in _args :
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# _params = _args['plugins']
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# if 'path' in _params and 'names' in _params :
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# loader = PluginLoader(**_params)
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# elif type(_params) == list:
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# loader = PluginLoader()
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# for _delegate in _params :
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# loader.set(_delegate)
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_plugins = None if 'plugins' not in _args else _args['plugins']
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# if registry.has('logger') :
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# _kwa = registry.get('logger')
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# _lmodule = getPROVIDERS[_kwa['provider']]
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if ( ('label' in _args and _args['label'] != 'logger') and registry.has('logger')):
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#
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# We did not request label called logger, so we are setting up a logger if it is specified in the registry
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#
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_kwargs = registry.get('logger')
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_kwargs['context'] = 'write'
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_kwargs['table'] =_module.__name__.split('.')[-1]+'_logs'
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# _logger = instance(**_kwargs)
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_module = PROVIDERS[_kwargs['provider']]['module']
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_logger = getattr(_module,'Writer')
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_logger = _logger(**_kwargs)
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else:
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_logger = None
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_kwargs = {'agent':_agent,'plugins':_plugins,'logger':_logger}
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if 'args' in _args :
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_kwargs['args'] = _args['args']
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# _datatransport = IReader(_agent,_plugins,_logger) if _context == 'read' else IWriter(_agent,_plugins,_logger)
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_datatransport = IReader(**_kwargs) if _context == 'read' else IWriter(**_kwargs)
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return _datatransport
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else:
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#
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# We can handle the case for an ETL object
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#
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raise Exception ("Missing or Unknown provider")
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pass
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class get :
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"""
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This class is just a wrapper to make the interface (API) more conversational and easy to understand
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"""
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@staticmethod
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def reader (**_args):
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if not _args or ('provider' not in _args and 'label' not in _args):
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_args['label'] = 'default'
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_args['context'] = 'read'
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# return instance(**_args)
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# _args['logger'] = instance(**{'label':'logger','context':'write','table':'logs'})
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_handler = instance(**_args)
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# _handler.setLogger(get.logger())
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return _handler
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@staticmethod
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def writer(**_args):
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"""
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This function is a wrapper that will return a writer to a database. It disambiguates the interface
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"""
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if not _args or ('provider' not in _args and 'label' not in _args):
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_args['label'] = 'default'
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_args['context'] = 'write'
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# _args['logger'] = instance(**{'label':'logger','context':'write','table':'logs'})
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_handler = instance(**_args)
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#
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# Implementing logging with the 'eat-your-own-dog-food' approach
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# Using dependency injection to set the logger (problem with imports)
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#
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# _handler.setLogger(get.logger())
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return _handler
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@staticmethod
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def logger ():
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if registry.has('logger') :
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_args = registry.get('logger')
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_args['context'] = 'write'
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return instance(**_args)
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return None
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@staticmethod
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def etl (**_args):
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if 'source' in _args and 'target' in _args :
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return IETL(**_args)
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else:
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raise Exception ("Malformed input found, object must have both 'source' and 'target' attributes")
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def supported ():
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_info = {}
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for _provider in PROVIDERS :
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_item = PROVIDERS[_provider]
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if _item['type'] not in _info :
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_info[_item['type']] = []
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_info[_item['type']].append(_provider)
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_df = pd.DataFrame()
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for _id in _info :
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if not _df.shape[0] :
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_df = pd.DataFrame(_info[_id],columns=[_id.replace('transport.','')])
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else:
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_df = pd.DataFrame(_info[_id],columns=[_id.replace('transport.','')]).join(_df, how='outer')
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return _df.fillna('')
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class factory :
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pass
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factory.instance = instance
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init()
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