hiplab/data-transport
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data-transport
mirror of https://github.com/lnyemba/data-transport
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refactor: factory, etl, fixes: session

This commit is contained in:
Steve Nyemba 2023-09-29 20:27:53 -05:00
parent 324d81bd16
commit 3f7f3d7306
10 changed files with 605 additions and 355 deletions
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174
bin/transport
View File

@ -14,19 +14,27 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
Usage : Usage :
transport --config <path-to-file.json> --procs <number-procs> transport help -- will print this page
@TODO: Create tables if they don't exist for relational databases
example of configuration :
1. Move data from a folder to a data-store transport move <path> [index]
transport [--folder <path> ] --config <config.json> #-- assuming the configuration doesn't have folder <path> path to the configuration file
transport --folder <path> --provider <postgresql|mongo|sqlite> --<database|db> <name> --table|doc <document_name> <index> optional index within the configuration file
In this case the configuration should look like :
{folder:..., target:{}} e.g: configuration file (JSON formatted)
2. Move data from one source to another - single source to a single target
transport --config <file.json>
{source:{..},target:{..}} or [{source:{..},target:{..}},{source:{..},target:{..}}] {"source":{"provider":"http","url":"https://cdn.wsform.com/wp-content/uploads/2020/06/agreement.csv"}
"target":{"provider":"sqlite3","path":"transport-demo.sqlite","table":"agreement"}
}
- single source to multiple targets
{
"source":{"provider":"http","url":"https://cdn.wsform.com/wp-content/uploads/2020/06/agreement.csv"},
"target":[
{"provider":"sqlite3","path":"transport-demo.sqlite","table":"agreement},
{"provider":"mongodb","db":"transport-demo","collection":"agreement"}
]
}
""" """
import pandas as pd import pandas as pd
@ -36,51 +44,111 @@ import sys
import transport import transport
import time import time
from multiprocessing import Process from multiprocessing import Process
SYS_ARGS = {} import typer
if len(sys.argv) > 1: import os
from transport import etl
from transport import providers
# SYS_ARGS = {}
# if len(sys.argv) > 1:
N = len(sys.argv) # N = len(sys.argv)
for i in range(1,N): # for i in range(1,N):
value = None # value = None
if sys.argv[i].startswith('--'): # if sys.argv[i].startswith('--'):
key = sys.argv[i][2:] #.replace('-','') # key = sys.argv[i][2:] #.replace('-','')
SYS_ARGS[key] = 1 # SYS_ARGS[key] = 1
if i + 1 < N: # if i + 1 < N:
value = sys.argv[i + 1] = sys.argv[i+1].strip() # value = sys.argv[i + 1] = sys.argv[i+1].strip()
if key and value and not value.startswith('--'): # if key and value and not value.startswith('--'):
SYS_ARGS[key] = value # SYS_ARGS[key] = value
i += 2 # i += 2
if __name__ == '__main__' : app = typer.Typer()
#
# Load information from the file ... # @app.command()
if 'help' in SYS_ARGS : def help() :
print (__doc__) print (__doc__)
else: def wait(jobs):
try: while jobs :
_info = json.loads(open(SYS_ARGS['config']).read()) jobs = [thread for thread in jobs if thread.is_alive()]
if 'index' in SYS_ARGS : time.sleep(1)
_index = int(SYS_ARGS['index'])
_info = [_item for _item in _info if _info.index(_item) == _index] @app.command()
pass def move (path,index=None):
elif 'id' in SYS_ARGS :
_info = [_item for _item in _info if 'id' in _item and _item['id'] == SYS_ARGS['id']] _proxy = lambda _object: _object.write(_object.read())
if os.path.exists(path):
file = open(path)
_config = json.loads (file.read() )
file.close()
if index :
_config = _config[ int(index)]
etl.instance(**_config)
else:
etl.instance(_config)
#
# if type(_config) == dict :
# _object = transport.etl.instance(**_config)
# _proxy(_object)
# else:
# #
# # here we are dealing with a list of objects (long ass etl job)
# jobs = []
# failed = []
# for _args in _config :
# if index and _config.index(_args) != index :
# continue
# _object=transport.etl.instance(**_args)
# thread = Process(target=_proxy,args=(_object,))
# thread.start()
# jobs.append(thread())
# if _config.index(_args) == 0 :
# thread.join()
wait(jobs)
@app.command()
def generate (path:str):
__doc__="""
"""
_config = [{"source":{"provider":"http","url":"https://cdn.wsform.com/wp-content/uploads/2020/06/agreement.csv"},"target":{"provider":"file","path":"addresses.csv","delimiter":"csv"}}]
file = open(path,'w')
file.write(json.dumps(_config))
file.close()
# if __name__ == '__main__' :
# #
# # Load information from the file ...
# if 'help' in SYS_ARGS :
# print (__doc__)
# else:
# try:
# _info = json.loads(open(SYS_ARGS['config']).read())
# if 'index' in SYS_ARGS :
# _index = int(SYS_ARGS['index'])
# _info = [_item for _item in _info if _info.index(_item) == _index]
# pass
# elif 'id' in SYS_ARGS :
# _info = [_item for _item in _info if 'id' in _item and _item['id'] == SYS_ARGS['id']]
procs = 1 if 'procs' not in SYS_ARGS else int(SYS_ARGS['procs']) # procs = 1 if 'procs' not in SYS_ARGS else int(SYS_ARGS['procs'])
jobs = transport.factory.instance(provider='etl',info=_info,procs=procs) # jobs = transport.factory.instance(provider='etl',info=_info,procs=procs)
print ([len(jobs),' Jobs are running']) # print ([len(jobs),' Jobs are running'])
N = len(jobs) # N = len(jobs)
while jobs : # while jobs :
x = len(jobs) # x = len(jobs)
jobs = [_job for _job in jobs if _job.is_alive()] # jobs = [_job for _job in jobs if _job.is_alive()]
if x != len(jobs) : # if x != len(jobs) :
print ([len(jobs),'... jobs still running']) # print ([len(jobs),'... jobs still running'])
time.sleep(1) # time.sleep(1)
print ([N,' Finished running']) # print ([N,' Finished running'])
except Exception as e: # except Exception as e:
print (e) # print (e)

2
setup.py
View File

@ -17,7 +17,7 @@ args = {
"license":"MIT", "license":"MIT",
"packages":["transport"]} "packages":["transport"]}
args["keywords"]=['mongodb','couchdb','rabbitmq','file','read','write','s3','sqlite'] args["keywords"]=['mongodb','couchdb','rabbitmq','file','read','write','s3','sqlite']
args["install_requires"] = ['pymongo','sqlalchemy<2.0.0','pandas','pandas-gbq','numpy','cloudant','pika','nzpy','boto3','boto','pyarrow','google-cloud-bigquery','google-cloud-bigquery-storage','flask-session','smart_open','botocore','psycopg2-binary','mysql-connector-python'] args["install_requires"] = ['pymongo','sqlalchemy<2.0.0','pandas','typer','pandas-gbq','numpy','cloudant','pika','nzpy','boto3','boto','pyarrow','google-cloud-bigquery','google-cloud-bigquery-storage','flask-session','smart_open','botocore','psycopg2-binary','mysql-connector-python']
args["url"] = "https://healthcareio.the-phi.com/git/code/transport.git" args["url"] = "https://healthcareio.the-phi.com/git/code/transport.git"
args['scripts'] = ['bin/transport'] args['scripts'] = ['bin/transport']
if sys.version_info[0] == 2 : if sys.version_info[0] == 2 :

113
transport/__init__.py
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@ -28,7 +28,7 @@ import importlib
import sys import sys
import sqlalchemy import sqlalchemy
if sys.version_info[0] > 2 : if sys.version_info[0] > 2 :
from transport.common import Reader, Writer,Console #, factory # from transport.common import Reader, Writer,Console #, factory
from transport import disk from transport import disk
from transport import s3 as s3 from transport import s3 as s3
@ -97,7 +97,7 @@ class factory :
TYPE = {"sql":{"providers":["postgresql","mysql","neteeza","bigquery","mariadb","redshift"]}} TYPE = {"sql":{"providers":["postgresql","mysql","neteeza","bigquery","mariadb","redshift"]}}
PROVIDERS = { PROVIDERS = {
"etl":{"class":{"read":etl.instance,"write":etl.instance}}, "etl":{"class":{"read":etl.instance,"write":etl.instance}},
"console":{"class":{"write":Console,"read":Console}}, # "console":{"class":{"write":Console,"read":Console}},
"file":{"class":{"read":disk.DiskReader,"write":disk.DiskWriter}}, "file":{"class":{"read":disk.DiskReader,"write":disk.DiskWriter}},
"sqlite":{"class":{"read":disk.SQLiteReader,"write":disk.SQLiteWriter}}, "sqlite":{"class":{"read":disk.SQLiteReader,"write":disk.SQLiteWriter}},
"postgresql":{"port":5432,"host":"localhost","database":None,"driver":pg,"default":{"type":"VARCHAR"},"class":{"read":sql.SQLReader,"write":sql.SQLWriter}}, "postgresql":{"port":5432,"host":"localhost","database":None,"driver":pg,"default":{"type":"VARCHAR"},"class":{"read":sql.SQLReader,"write":sql.SQLWriter}},
@ -124,6 +124,9 @@ class factory :
# #
# Legacy code being returned # Legacy code being returned
return factory._instance(**_args); return factory._instance(**_args);
else: else:
return instance(**_args) return instance(**_args)
@staticmethod @staticmethod
@ -175,22 +178,31 @@ def instance(**_pargs):
file.close() file.close()
_provider = _args['provider'] _provider = _args['provider']
_group = None _context = list( set(['read','write','listen']) & set(_args.keys()) )
if _context :
_context = _context[0]
else:
_context = _args['context'] if 'context' in _args else 'read'
# _group = None
for _id in providers.CATEGORIES : # for _id in providers.CATEGORIES :
if _provider in providers.CATEGORIES[_id] : # if _provider in providers.CATEGORIES[_id] :
_group = _id # _group = _id
break # break
if _group : # if _group :
if _provider in providers.PROVIDERS and _context in providers.PROVIDERS[_provider]:
_classPointer = _getClassInstance(_group,**_args) # _classPointer = _getClassInstance(_group,**_args)
_classPointer = providers.PROVIDERS[_provider][_context]
# #
# Let us reformat the arguments # Let us reformat the arguments
if 'read' in _args or 'write' in _args : # if 'read' in _args or 'write' in _args :
_args = _args['read'] if 'read' in _args else _args['write'] # _args = _args['read'] if 'read' in _args else _args['write']
_args['provider'] = _provider # _args['provider'] = _provider
if _group == 'sql' : # if _group == 'sql' :
if _provider in providers.CATEGORIES['sql'] :
_info = _get_alchemyEngine(**_args) _info = _get_alchemyEngine(**_args)
_args = dict(_args,**_info) _args = dict(_args,**_info)
@ -215,57 +227,68 @@ def _get_alchemyEngine(**_args):
This function returns the SQLAlchemy engine associated with parameters, This is only applicable for SQL _items This function returns the SQLAlchemy engine associated with parameters, This is only applicable for SQL _items
:_args arguments passed to the factory {provider and other} :_args arguments passed to the factory {provider and other}
""" """
#@TODO: Enable authentication files (private_key)
_username = _args['username'] if 'username' in _args else ''
_password = _args['password'] if 'password' in _args else ''
_account = _args['account'] if 'account' in _args else ''
_database = _args['database']
_provider = _args['provider'] _provider = _args['provider']
if _username != '': _pargs = {}
_account = _username + ':'+_password+'@' if _provider == providers.SQLITE3 :
_host = _args['host'] if 'host' in _args else '' _path = _args['database'] if 'database' in _args else _args['path']
_port = _args['port'] if 'port' in _args else '' uri = ''.join([_provider,':///',_path])
if _provider in providers.DEFAULT :
_default = providers.DEFAULT[_provider]
_host = _host if _host != '' else (_default['host'] if 'host' in _default else '')
_port = _port if _port != '' else (_default['port'] if 'port' in _default else '')
if _port == '':
_port = providers.DEFAULT['port'] if 'port' in providers.DEFAULT else ''
#
if _host != '' and _port != '' :
_fhost = _host+":"+str(_port) #--formatted hostname
else: else:
_fhost = _host
# Let us update the parameters we have thus far #@TODO: Enable authentication files (private_key)
_username = _args['username'] if 'username' in _args else ''
_password = _args['password'] if 'password' in _args else ''
_account = _args['account'] if 'account' in _args else ''
_database = _args['database'] if 'database' in _args else _args['path']
if _username != '':
_account = _username + ':'+_password+'@'
_host = _args['host'] if 'host' in _args else ''
_port = _args['port'] if 'port' in _args else ''
if _provider in providers.DEFAULT :
_default = providers.DEFAULT[_provider]
_host = _host if _host != '' else (_default['host'] if 'host' in _default else '')
_port = _port if _port != '' else (_default['port'] if 'port' in _default else '')
if _port == '':
_port = providers.DEFAULT['port'] if 'port' in providers.DEFAULT else ''
#
if _host != '' and _port != '' :
_fhost = _host+":"+str(_port) #--formatted hostname
else:
_fhost = _host
# Let us update the parameters we have thus far
# #
uri = ''.join([_provider,"://",_account,_fhost,'/',_database]) uri = ''.join([_provider,"://",_account,_fhost,'/',_database])
_pargs = {'host':_host,'port':_port,'username':_username,'password':_password}
_engine = sqlalchemy.create_engine (uri,future=True) _engine = sqlalchemy.create_engine (uri,future=True)
_out = {'sqlalchemy':_engine} _out = {'sqlalchemy':_engine}
_pargs = {'host':_host,'port':_port,'username':_username,'password':_password}
for key in _pargs : for key in _pargs :
if _pargs[key] != '' : if _pargs[key] != '' :
_out[key] = _pargs[key] _out[key] = _pargs[key]
return _out return _out
@DeprecationWarning
def _getClassInstance(_group,**_args): def _getClassInstance(_group,**_args):
""" """
This function returns the class instance we are attempting to instanciate This function returns the class instance we are attempting to instanciate
:_group items in providers.CATEGORIES.keys() :_group items in providers.CATEGORIES.keys()
:_args arguments passed to the factory class :_args arguments passed to the factory class
""" """
if 'read' in _args or 'write' in _args : # if 'read' in _args or 'write' in _args :
_context = 'read' if 'read' in _args else _args['write'] # _context = 'read' if 'read' in _args else _args['write']
_info = _args[_context] # _info = _args[_context]
else: # else:
_context = _args['context'] if 'context' in _args else 'read' # _context = _args['context'] if 'context' in _args else 'read'
_class = providers.READ[_group] if _context == 'read' else providers.WRITE[_group] # _class = providers.READ[_group] if _context == 'read' else providers.WRITE[_group]
if type(_class) == dict and _args['provider'] in _class: # if type(_class) == dict and _args['provider'] in _class:
_class = _class[_args['provider']] # _class = _class[_args['provider']]
return _class # return _class
@DeprecationWarning
def __instance(**_args): def __instance(**_args):
""" """

46
transport/common.py
View File

@ -93,29 +93,29 @@ class ReadWriter(Reader,Writer) :
This class implements the read/write functions aggregated This class implements the read/write functions aggregated
""" """
pass pass
class Console(Writer): # class Console(Writer):
lock = RLock() # lock = RLock()
def __init__(self,**_args): # def __init__(self,**_args):
self.lock = _args['lock'] if 'lock' in _args else False # self.lock = _args['lock'] if 'lock' in _args else False
self.info = self.write # self.info = self.write
self.debug = self.write # self.debug = self.write
self.log = self.write # self.log = self.write
pass # pass
def write (self,logs=None,**_args): # def write (self,logs=None,**_args):
if self.lock : # if self.lock :
Console.lock.acquire() # Console.lock.acquire()
try: # try:
_params = _args if logs is None and _args else logs # _params = _args if logs is None and _args else logs
if type(_params) == list: # if type(_params) == list:
for row in _params : # for row in _params :
print (row) # print (row)
else: # else:
print (_params) # print (_params)
except Exception as e : # except Exception as e :
print (e) # print (e)
finally: # finally:
if self.lock : # if self.lock :
Console.lock.release() # Console.lock.release()
""" """

463
transport/etl.py
View File

@ -35,6 +35,9 @@ import json
import sys import sys
import transport import transport
import time import time
import os
from multiprocessing import Process from multiprocessing import Process
SYS_ARGS = {} SYS_ARGS = {}
if len(sys.argv) > 1: if len(sys.argv) > 1:
@ -52,199 +55,301 @@ if len(sys.argv) > 1:
i += 2 i += 2
class Transporter(Process):
class Post(Process): """
def __init__(self,**args): The transporter (Jason Stathem) moves data from one persistant store to another
super().__init__() - callback functions
self.store = args['target'] :onFinish callback function when finished
if 'provider' not in args['target'] : :onError callback function when an error occurs
pass :source source data specification
self.PROVIDER = args['target']['type'] :target destination(s) to move the data to
# self.writer = transport.factory.instance(**args['target']) """
else:
self.PROVIDER = args['target']['provider']
self.store['context'] = 'write'
# self.store = args['target']
self.store['lock'] = True
# self.writer = transport.instance(**args['target'])
#
# If the table doesn't exists maybe create it ?
#
self.rows = args['rows']
# self.rows = args['rows'].fillna('')
def log(self,**_args) :
if ETL.logger :
ETL.logger.info(**_args)
def run(self):
_info = {"values":self.rows} if 'couch' in self.PROVIDER else self.rows
writer = transport.factory.instance(**self.store)
writer.write(_info)
writer.close()
class ETL (Process):
logger = None
def __init__(self,**_args): def __init__(self,**_args):
super().__init__() super().__init__()
# self.onfinish = _args['onFinish']
self.name = _args['id'] if 'id' in _args else 'UNREGISTERED' # self._onerror = _args['onError']
# if 'provider' not in _args['source'] : self._source = _args['source']
# #@deprecate
# self.reader = transport.factory.instance(**_args['source'])
# else:
# #
# # This is the new interface
# _args['source']['context'] = 'read'
# self.reader = transport.instance(**_args['source'])
#
# do we have an sql query provided or not ....
# self.sql = _args['source']['sql'] if 'sql' in _args['source'] else None
# self.cmd = _args['source']['cmd'] if 'cmd' in _args['source'] else None
# self._oargs = _args['target'] #transport.factory.instance(**_args['target'])
self._source = _args ['source']
self._target = _args['target'] self._target = _args['target']
self._source['context'] = 'read'
self._target['context'] = 'write' #
# Let's insure we can support multiple targets
self._target = [self._target] if type(self._target) != list else self._target
self.JOB_COUNT = _args['jobs'] pass
self.jobs = [] def read(self,**_args):
# self.logger = transport.factory.instance(**_args['logger']) """
def log(self,**_args) : This function
if ETL.logger : """
ETL.logger.info(**_args) _reader = transport.factory.instance(**self._source)
#
# If arguments are provided then a query is to be executed (not just a table dump)
return _reader.read() if 'args' not in self._source else _reader.read(**self._source['args'])
def run(self): def _delegate_write(self,_data,**_args):
# if self.cmd : """
# idf = self.reader.read(**self.cmd) This function will write a data-frame to a designated data-store, The function is built around a delegation design pattern
# else: :data data-frame or object to be written
# idf = self.reader.read() """
# idf = pd.DataFrame(idf) for _target in self._target :
# # idf = idf.replace({np.nan: None}, inplace = True) if 'write' not in _target :
_target['context'] = 'write'
_target['lock'] = True
else:
_target['write']['lock'] = True
_writer = transport.factory.instance(**_target)
_writer.write(_data,**_args)
if hasattr(_writer,'close') :
_writer.close()
def write(self,_df,**_args):
"""
"""
SEGMENT_COUNT = 6
MAX_ROWS = 1000000
# _df = self.read()
_segments = np.array_split(np.range(_df.shape[0]),SEGMENT_COUNT) if _df.shape[0] > MAX_ROWS else np.array( [np.arange(_df.shape[0])])
# _index = 0
for _indexes in _segments :
_fwd_args = {} if not _args else _args
self._delegate_write(_df.iloc[_indexes],**_fwd_args)
#
# @TODO: Perhaps consider writing up each segment in a thread/process (speeds things up?)
pass
# idf.columns = [str(name).replace("b'",'').replace("'","").strip() for name in idf.columns.tolist()] def instance(**_args):
# self.log(rows=idf.shape[0],cols=idf.shape[1],jobs=self.JOB_COUNT) _proxy = lambda _agent: _agent.write(_agent.read())
if 'source' in _args and 'target' in _args :
_agent = Transporter(**_args)
_proxy(_agent)
else:
_config = _args['config']
_items = [Transporter(**_item) for _item in _config ]
_MAX_JOBS = 5
_items = np.array_split(_items,_MAX_JOBS)
for _batch in _items :
jobs = []
for _item in _batch :
thread = Process(target=_proxy,args = (_item,))
thread.start()
jobs.append(thread)
while jobs :
jobs = [thread for thread in jobs if thread.is_alive()]
time.sleep(1)
pass
# class Post(Process):
# def __init__(self,**args):
# super().__init__()
# self.store = args['target']
# if 'provider' not in args['target'] :
# pass
# self.PROVIDER = args['target']['type']
# # self.writer = transport.factory.instance(**args['target'])
# else:
# self.PROVIDER = args['target']['provider']
# self.store['context'] = 'write'
# # self.store = args['target']
# self.store['lock'] = True
# # self.writer = transport.instance(**args['target'])
# #
# # If the table doesn't exists maybe create it ?
# #
# self.rows = args['rows']
# # self.rows = args['rows'].fillna('')
# def log(self,**_args) :
# if ETL.logger :
# ETL.logger.info(**_args)
# def run(self):
# _info = {"values":self.rows} if 'couch' in self.PROVIDER else self.rows
# writer = transport.factory.instance(**self.store)
# writer.write(_info)
# writer.close()
#
# writing the data to a designated data source # class ETL (Process):
# # logger = None
try: # def __init__(self,**_args):
# super().__init__()
# self.name = _args['id'] if 'id' in _args else 'UNREGISTERED'
# # if 'provider' not in _args['source'] :
# # #@deprecate
# # self.reader = transport.factory.instance(**_args['source'])
# # else:
# # #
# # # This is the new interface
# # _args['source']['context'] = 'read'
# # self.reader = transport.instance(**_args['source'])
# #
# # do we have an sql query provided or not ....
# # self.sql = _args['source']['sql'] if 'sql' in _args['source'] else None
# # self.cmd = _args['source']['cmd'] if 'cmd' in _args['source'] else None
# # self._oargs = _args['target'] #transport.factory.instance(**_args['target'])
# self._source = _args ['source']
# self._target = _args['target']
# self._source['context'] = 'read'
# self._target['context'] = 'write'
# self.JOB_COUNT = _args['jobs']
# self.jobs = []
# # self.logger = transport.factory.instance(**_args['logger'])
# def log(self,**_args) :
# if ETL.logger :
# ETL.logger.info(**_args)
# def run(self):
# # if self.cmd :
# # idf = self.reader.read(**self.cmd)
# # else:
# # idf = self.reader.read()
# # idf = pd.DataFrame(idf)
# # # idf = idf.replace({np.nan: None}, inplace = True)
# # idf.columns = [str(name).replace("b'",'').replace("'","").strip() for name in idf.columns.tolist()]
# # self.log(rows=idf.shape[0],cols=idf.shape[1],jobs=self.JOB_COUNT)
# #
# # writing the data to a designated data source
# #
# try:
_log = {"name":self.name,"rows":{"input":0,"output":0}} # _log = {"name":self.name,"rows":{"input":0,"output":0}}
_reader = transport.factory.instance(**self._source) # _reader = transport.factory.instance(**self._source)
if 'table' in self._source : # if 'table' in self._source :
_df = _reader.read() # _df = _reader.read()
else: # else:
_df = _reader.read(**self._source['cmd']) # _df = _reader.read(**self._source['cmd'])
_log['rows']['input'] = _df.shape[0] # _log['rows']['input'] = _df.shape[0]
# # #
# Let's write the input data-frame to the target ... # # Let's write the input data-frame to the target ...
_writer = transport.factory.instance(**self._target) # _writer = transport.factory.instance(**self._target)
_writer.write(_df) # _writer.write(_df)
_log['rows']['output'] = _df.shape[0] # _log['rows']['output'] = _df.shape[0]
# self.log(module='write',action='partitioning',jobs=self.JOB_COUNT) # # self.log(module='write',action='partitioning',jobs=self.JOB_COUNT)
# rows = np.array_split(np.arange(0,idf.shape[0]),self.JOB_COUNT) # # rows = np.array_split(np.arange(0,idf.shape[0]),self.JOB_COUNT)
# # # # #
# # @TODO: locks # # # @TODO: locks
# for i in np.arange(self.JOB_COUNT) : # # for i in np.arange(self.JOB_COUNT) :
# # _id = ' '.join([str(i),' table ',self.name]) # # # _id = ' '.join([str(i),' table ',self.name])
# indexes = rows[i] # # indexes = rows[i]
# segment = idf.loc[indexes,:].copy() #.to_dict(orient='records') # # segment = idf.loc[indexes,:].copy() #.to_dict(orient='records')
# _name = "partition-"+str(i) # # _name = "partition-"+str(i)
# if segment.shape[0] == 0 : # # if segment.shape[0] == 0 :
# continue # # continue
# proc = Post(target = self._oargs,rows = segment,name=_name) # # proc = Post(target = self._oargs,rows = segment,name=_name)
# self.jobs.append(proc) # # self.jobs.append(proc)
# proc.start() # # proc.start()
# self.log(module='write',action='working',segment=str(self.name),table=self.name,rows=segment.shape[0]) # # self.log(module='write',action='working',segment=str(self.name),table=self.name,rows=segment.shape[0])
# while self.jobs : # # while self.jobs :
# jobs = [job for job in proc if job.is_alive()] # # jobs = [job for job in proc if job.is_alive()]
# time.sleep(1) # # time.sleep(1)
except Exception as e: # except Exception as e:
print (e) # print (e)
self.log(**_log) # self.log(**_log)
def is_done(self): # def is_done(self):
self.jobs = [proc for proc in self.jobs if proc.is_alive()] # self.jobs = [proc for proc in self.jobs if proc.is_alive()]
return len(self.jobs) == 0 # return len(self.jobs) == 0
def instance(**_args):
"""
:path ,index, id # def instance (**_args):
:param _info list of objects with {source,target}` # """
:param logger # path to configuration file
""" # """
logger = _args['logger'] if 'logger' in _args else None # _path = _args['path']
if 'path' in _args : # _config = {}
_info = json.loads((open(_args['path'])).read()) # jobs = []
# if os.path.exists(_path) :
# file = open(_path)
if 'index' in _args : # _config = json.loads(file.read())
_index = int(_args['index']) # file.close()
_info = _info[_index] # if _config and type
elif 'id' in _args :
_info = [_item for _item in _info if '_id' in _item and _item['id'] == _args['id']]
_info = _info[0] if _info else _info
else:
_info = _args['info']
if logger and type(logger) != str:
ETL.logger = logger # def _instance(**_args):
elif logger == 'console': # """
ETL.logger = transport.factory.instance(provider='console',context='write',lock=True) # :path ,index, id
if type(_info) in [list,dict] : # :param _info list of objects with {source,target}`
_info = _info if type(_info) != dict else [_info] # :param logger
# # """
# The assumption here is that the objects within the list are {source,target} # logger = _args['logger'] if 'logger' in _args else None
jobs = [] # if 'path' in _args :
for _item in _info : # _info = json.loads((open(_args['path'])).read())
_item['jobs'] = 5 if 'procs' not in _args else int(_args['procs'])
_job = ETL(**_item)
_job.start()
jobs.append(_job)
return jobs
else:
return None # if 'index' in _args :
# _index = int(_args['index'])
if __name__ == '__main__' : # _info = _info[_index]
_info = json.loads(open (SYS_ARGS['config']).read())
index = int(SYS_ARGS['index']) if 'index' in SYS_ARGS else None
procs = []
for _config in _info :
if 'source' in SYS_ARGS :
_config['source'] = {"type":"disk.DiskReader","args":{"path":SYS_ARGS['source'],"delimiter":","}}
_config['jobs'] = 3 if 'jobs' not in SYS_ARGS else int(SYS_ARGS['jobs'])
etl = ETL (**_config)
if index is None:
etl.start() # elif 'id' in _args :
procs.append(etl) # _info = [_item for _item in _info if '_id' in _item and _item['id'] == _args['id']]
# _info = _info[0] if _info else _info
elif _info.index(_config) == index : # else:
# _info = _args['info']
# if logger and type(logger) != str:
# ETL.logger = logger
# elif logger == 'console':
# ETL.logger = transport.factory.instance(provider='console',context='write',lock=True)
# if type(_info) in [list,dict] :
# _info = _info if type(_info) != dict else [_info]
# #
# # The assumption here is that the objects within the list are {source,target}
# jobs = []
# for _item in _info :
# print (_config) # _item['jobs'] = 5 if 'procs' not in _args else int(_args['procs'])
procs = [etl] # _job = ETL(**_item)
etl.start()
break # _job.start()
# # jobs.append(_job)
# # return jobs
N = len(procs)
while procs : # else:
procs = [thread for thread in procs if not thread.is_done()] # return None
if len(procs) < N :
print (["Finished ",(N-len(procs)), " remaining ", len(procs)]) # if __name__ == '__main__' :
N = len(procs) # _info = json.loads(open (SYS_ARGS['config']).read())
time.sleep(1) # index = int(SYS_ARGS['index']) if 'index' in SYS_ARGS else None
# print ("We're done !!") # procs = []
# for _config in _info :
# if 'source' in SYS_ARGS :
# _config['source'] = {"type":"disk.DiskReader","args":{"path":SYS_ARGS['source'],"delimiter":","}}
# _config['jobs'] = 3 if 'jobs' not in SYS_ARGS else int(SYS_ARGS['jobs'])
# etl = ETL (**_config)
# if index is None:
# etl.start()
# procs.append(etl)
# elif _info.index(_config) == index :
# # print (_config)
# procs = [etl]
# etl.start()
# break
# #
# #
# N = len(procs)
# while procs :
# procs = [thread for thread in procs if not thread.is_done()]
# if len(procs) < N :
# print (["Finished ",(N-len(procs)), " remaining ", len(procs)])
# N = len(procs)
# time.sleep(1)
# # print ("We're done !!")

33
transport/providers.py
View File

@ -1,4 +1,4 @@
from transport.common import Reader, Writer,Console #, factory # from transport.common import Reader, Writer,Console #, factory
from transport import disk from transport import disk
import sqlite3 import sqlite3
from transport import s3 as s3 from transport import s3 as s3
@ -9,6 +9,7 @@ from transport import sql as sql
from transport import etl as etl from transport import etl as etl
from transport import qlistener from transport import qlistener
from transport import bricks from transport import bricks
from transport import session
import psycopg2 as pg import psycopg2 as pg
import mysql.connector as my import mysql.connector as my
from google.cloud import bigquery as bq from google.cloud import bigquery as bq
@ -33,6 +34,8 @@ MARIADB = 'mariadb'
COUCHDB = 'couch' COUCHDB = 'couch'
CONSOLE = 'console' CONSOLE = 'console'
ETL = 'etl' ETL = 'etl'
# #
# synonyms of the above # synonyms of the above
BQ = BIGQUERY BQ = BIGQUERY
@ -54,13 +57,37 @@ CATEGORIES ={'sql':[NETEZZA,PG,MYSQL,REDSHIFT,SQLITE,MARIADB],'nosql':[MONGODB,C
READ = {'sql':sql.SQLReader,'nosql':{MONGODB:mongo.MongoReader,COUCHDB:couch.CouchReader}, READ = {'sql':sql.SQLReader,'nosql':{MONGODB:mongo.MongoReader,COUCHDB:couch.CouchReader},
'cloud':{BIGQUERY:sql.BigQueryReader,DATABRICKS:bricks.BricksReader}, 'cloud':{BIGQUERY:sql.BigQueryReader,DATABRICKS:bricks.BricksReader},
'file':disk.DiskReader,'queue':{RABBIT:queue.QueueReader,QLISTENER:qlistener.qListener}, 'file':disk.DiskReader,'queue':{RABBIT:queue.QueueReader,QLISTENER:qlistener.qListener},
'cli':{CONSOLE:Console},'memory':{CONSOLE:Console} # 'cli':{CONSOLE:Console},'memory':{CONSOLE:Console},'http':session.HttpReader
} }
WRITE = {'sql':sql.SQLWriter,'nosql':{MONGODB:mongo.MongoWriter,COUCHDB:couch.CouchWriter}, WRITE = {'sql':sql.SQLWriter,'nosql':{MONGODB:mongo.MongoWriter,COUCHDB:couch.CouchWriter},
'cloud':{BIGQUERY:sql.BigQueryWriter,DATABRICKS:bricks.BricksWriter}, 'cloud':{BIGQUERY:sql.BigQueryWriter,DATABRICKS:bricks.BricksWriter},
'file':disk.DiskWriter,'queue':{RABBIT:queue.QueueWriter,QLISTENER:qlistener.qListener},'cli':{CONSOLE:Console},'memory':{CONSOLE:Console} 'file':disk.DiskWriter,'queue':{RABBIT:queue.QueueWriter,QLISTENER:qlistener.qListener},
# 'cli':{CONSOLE:Console},
# 'memory':{CONSOLE:Console}, 'http':session.HttpReader
} }
# SQL_PROVIDERS = [POSTGRESQL,MYSQL,NETEZZA,MARIADB,SQLITE]
PROVIDERS = {
FILE:{'read':disk.DiskReader,'write':disk.DiskWriter},
SQLITE:{'read':disk.SQLiteReader,'write':disk.SQLiteWriter,'driver':sqlite3},
POSTGRESQL:{'read':sql.SQLReader,'write':sql.SQLWriter,'driver':pg,'default':{'host':'localhost','port':5432}},
NETEZZA:{'read':sql.SQLReader,'write':sql.SQLWriter,'driver':nz,'default':{'port':5480}},
REDSHIFT:{'read':sql.SQLReader,'write':sql.SQLWriter,'driver':pg,'default':{'host':'localhost','port':5432}},
RABBITMQ:{'read':queue.QueueReader,'writer':queue.QueueWriter,'context':queue.QueueListener,'default':{'host':'localhost','port':5432}},
MYSQL:{'read':sql.SQLReader,'write':sql.SQLWriter,'driver':my,'default':{'host':'localhost','port':3306}},
MARIADB:{'read':sql.SQLReader,'write':sql.SQLWriter,'driver':my,'default':{'host':'localhost','port':3306}},
S3:{'read':s3.s3Reader,'write':s3.s3Writer},
BIGQUERY:{'read':sql.BigQueryReader,'write':sql.BigQueryWriter},
QLISTENER:{'read':qlistener.qListener,'write':qlistener.qListener,'default':{'host':'localhost','port':5672}},
CONSOLE:{'read':qlistener.Console,"write":qlistener.Console},
HTTP:{'read':session.HttpReader,'write':session.HttpWriter},
DATABRICKS:{'read':bricks.BricksReader,'write':bricks.BricksWriter},
MONGODB:{'read':mongo.MongoReader,'write':mongo.MongoWriter,'default':{'port':27017,'host':'localhost'}},
COUCHDB:{'read':couch.CouchReader,'writer':couch.CouchWriter,'default':{'host':'localhost','port':5984}},
ETL :{'read':etl.Transporter,'write':etl.Transporter}
}
DEFAULT = {PG:{'host':'localhost','port':5432},MYSQL:{'host':'localhost','port':3306}} DEFAULT = {PG:{'host':'localhost','port':5432},MYSQL:{'host':'localhost','port':3306}}
DEFAULT[MONGODB] = {'port':27017,'host':'localhost'} DEFAULT[MONGODB] = {'port':27017,'host':'localhost'}
DEFAULT[REDSHIFT] = DEFAULT[PG] DEFAULT[REDSHIFT] = DEFAULT[PG]

5
transport/qlistener.py
View File

@ -40,3 +40,8 @@ class qListener :
_q = qListener._queue[_id] _q = qListener._queue[_id]
_q.put(_data) _q.put(_data)
_q.join() _q.join()
class Console (qListener):
def __init__(self,**_args):
super().__init__(callback=print)
# self.callback = print

100
transport/session.py
View File

@ -1,54 +1,60 @@
from flask import request, session from flask import request, session
from datetime import datetime from datetime import datetime
import re import re
from common import Reader, Writer from transport.common import Reader, Writer
import json import json
import requests
from io import StringIO
import pandas as pd
class HttpRequestReader(Reader):
class HttpReader(Reader):
""" """
This class is designed to read data from an Http request file handler provided to us by flask This class is designed to read data from an Http request file handler provided to us by flask
The file will be heald in memory and processed accordingly The file will be heald in memory and processed accordingly
NOTE: This is inefficient and can crash a micro-instance (becareful) NOTE: This is inefficient and can crash a micro-instance (becareful)
""" """
def __init__(self,**params): def __init__(self,**_args):
self.file_length = 0 self._url = _args['url']
try: self._headers = None if 'headers' not in _args else _args['headers']
#self.file = params['file'] # def isready(self):
#self.file.seek(0, os.SEEK_END) # return self.file_length > 0
#self.file_length = self.file.tell() def format(self,_response):
_mimetype= _response.headers['Content-Type']
#print 'size of file ',self.file_length if _mimetype == 'text/csv' or 'text/csv':
self.content = params['file'].readlines() _content = _response.text
self.file_length = len(self.content) return pd.read_csv(StringIO(_content))
except Exception as e: #
print ("Error ... ",e) # @TODO: Add support for excel, JSON and other file formats that fit into a data-frame
pass #
def isready(self): return _response.text
return self.file_length > 0 def read(self,**_args):
def read(self,size =-1): if self._headers :
i = 1 r = requests.get(self._url,headers = self._headers)
for row in self.content: else:
i += 1 r = requests.get(self._url,headers = self._headers)
if size == i: return self.format(r)
break
yield row
class HttpSessionWriter(Writer): class HttpWriter(Writer):
""" """
This class is designed to write data to a session/cookie This class is designed to submit data to an endpoint (url)
""" """
def __init__(self,**params): def __init__(self,**_args):
""" """
@param key required session key @param key required session key
""" """
self.session = params['queue'] self._url = _args['url']
self.session['sql'] = [] self._name = _args['name']
self.session['csv'] = [] self._method = 'post' if 'method' not in _args else _args['method']
self.tablename = re.sub('..+$','',params['filename'])
self.session['uid'] = params['uid'] # self.session = params['queue']
# self.session['sql'] = []
# self.session['csv'] = []
# self.tablename = re.sub('..+$','',params['filename'])
# self.session['uid'] = params['uid']
#self.xchar = params['xchar'] #self.xchar = params['xchar']
@ -57,10 +63,26 @@ class HttpSessionWriter(Writer):
return "".join(["INSERT INTO :table VALUES('",values,"');\n"]).replace(':table',self.tablename) return "".join(["INSERT INTO :table VALUES('",values,"');\n"]).replace(':table',self.tablename)
def isready(self): def isready(self):
return True return True
def write(self,**params): def write(self,_data,**_args):
label = params['label'] #
row = params ['row'] #
_method = self._method if 'method' not in _args else _args['method']
_method = _method.lower()
_mimetype = 'text/csv'
if type(_data) == dict :
_mimetype = 'application/json'
_content = _data
else:
_content = _data.to_dict(orient='records')
_headers = {'Content-Type':_mimetype}
_pointer = getattr(requests,_method)
if label == 'usable': _pointer ({self._name:_content},headers=_headers)
self.session['csv'].append(self.format(row,','))
self.session['sql'].append(self.format_sql(row))
# label = params['label']
# row = params ['row']
# if label == 'usable':
# self.session['csv'].append(self.format(row,','))
# self.session['sql'].append(self.format_sql(row))

22
transport/sql.py
View File

@ -291,17 +291,17 @@ class SQLWriter(SQLRW,Writer):
""" """
# inspect = False if 'inspect' not in _args else _args['inspect'] # inspect = False if 'inspect' not in _args else _args['inspect']
# cast = False if 'cast' not in _args else _args['cast'] # cast = False if 'cast' not in _args else _args['cast']
if not self.fields : # if not self.fields :
if type(info) == list : # if type(info) == list :
_fields = info[0].keys() # _fields = info[0].keys()
elif type(info) == dict : # elif type(info) == dict :
_fields = info.keys() # _fields = info.keys()
elif type(info) == pd.DataFrame : # elif type(info) == pd.DataFrame :
_fields = info.columns.tolist() # _fields = info.columns.tolist()
# _fields = info.keys() if type(info) == dict else info[0].keys() # # _fields = info.keys() if type(info) == dict else info[0].keys()
_fields = list (_fields) # # _fields = list (_fields)
self.init(_fields) # self.init(_fields)
try: try:
table = _args['table'] if 'table' in _args else self.table table = _args['table'] if 'table' in _args else self.table

2
transport/version.py
View File

@ -1,2 +1,2 @@
__author__ = 'The Phi Technology' __author__ = 'The Phi Technology'
__version__= '1.8.6' __version__= '1.9.0'