bug fixes and enhancements, added console output(for logging)
This commit is contained in:
Steve Nyemba
parent
6c406407b2
commit
98eaa99820
157
bin/transport
157
bin/transport
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@ -53,148 +53,29 @@ if len(sys.argv) > 1:
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i += 2
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class Post(Process):
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def __init__(self,**args):
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super().__init__()
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if 'provider' not in args['target'] :
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self.PROVIDER = args['target']['type']
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self.writer = transport.factory.instance(**args['target'])
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if __name__ == '__main__' :
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#
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# Load information from the file ...
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if 'help' in SYS_ARGS :
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print (__doc__)
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else:
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self.PROVIDER = args['target']['provider']
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args['target']['context'] = 'write'
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self.store = args['target']
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# self.writer = transport.instance(**args['target'])
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#
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# If the table doesn't exists maybe create it ?
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#
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self.rows = args['rows'].fillna('')
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def run(self):
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_info = {"values":self.rows} if 'couch' in self.PROVIDER else self.rows
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ltypes = self.rows.dtypes.values
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columns = self.rows.dtypes.index.tolist()
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# if not self.writer.has() :
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# self.writer.make(fields=columns)
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# self.log(module='write',action='make-table',input={"name":self.writer.table})
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for name in columns :
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if _info[name].dtype in ['int32','int64','int','float','float32','float64'] :
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value = 0
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else:
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value = ''
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_info[name] = _info[name].fillna(value)
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writer = transport.factory.instance(**self.store)
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writer.write(_info)
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writer.close()
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class ETL (Process):
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def __init__(self,**_args):
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super().__init__()
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self.name = _args['id']
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if 'provider' not in _args['source'] :
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#@deprecate
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self.reader = transport.factory.instance(**_args['source'])
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else:
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#
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# This is the new interface
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_args['source']['context'] = 'read'
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self.reader = transport.instance(**_args['source'])
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#
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# do we have an sql query provided or not ....
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# self.sql = _args['source']['sql'] if 'sql' in _args['source'] else None
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self.cmd = _args['source']['cmd'] if 'cmd' in _args['source'] else None
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self._oargs = _args['target'] #transport.factory.instance(**_args['target'])
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self.JOB_COUNT = _args['jobs']
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self.jobs = []
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# self.logger = transport.factory.instance(**_args['logger'])
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def log(self,**_args) :
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_args['name'] = self.name
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print (_args)
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def run(self):
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if self.cmd :
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idf = self.reader.read(**self.cmd)
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else:
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idf = self.reader.read()
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idf = pd.DataFrame(idf)
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# idf = idf.replace({np.nan: None}, inplace = True)
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idf.columns = [str(name).replace("b'",'').replace("'","").strip() for name in idf.columns.tolist()]
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self.log(rows=idf.shape[0],cols=idf.shape[1],jobs=self.JOB_COUNT)
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#
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# writing the data to a designated data source
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#
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try:
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_info = json.loads(open(SYS_ARGS['config']).read())
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if 'index' in SYS_ARGS :
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_index = int(SYS_ARGS['index'])
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_info = [_item for _item in _info if _info.index(_item) == _index]
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pass
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self.log(module='write',action='partitioning')
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rows = np.array_split(np.arange(0,idf.shape[0]),self.JOB_COUNT)
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#
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# @TODO: locks
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for i in np.arange(self.JOB_COUNT) :
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_id = 'segment # '.join([str(i),' ',self.name])
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indexes = rows[i]
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segment = idf.loc[indexes,:].copy() #.to_dict(orient='records')
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if segment.shape[0] == 0 :
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continue
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proc = Post(target = self._oargs,rows = segment,name=_id)
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self.jobs.append(proc)
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proc.start()
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self.log(module='write',action='working',segment=_id)
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# while poc :
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# proc = [job for job in proc if job.is_alive()]
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# time.sleep(1)
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procs = 1 if 'procs' not in SYS_ARGS else int(SYS_ARGS['procs'])
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jobs = transport.factory.instance(provider='etl',info=_info,procs=procs)
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while jobs :
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x = len(jobs)
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jobs = [_job for _job in jobs if _job.is_alive()]
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if x != len(jobs) :
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print ([len(jobs),'... jobs running'])
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time.sleep(1)
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except Exception as e:
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print (e)
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def is_done(self):
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self.jobs = [proc for proc in self.jobs if proc.is_alive()]
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return len(self.jobs) == 0
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def apply(_args) :
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"""
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This function will apply a set of commands against a data-store. The expected structure is as follows :
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{"store":...,"apply":[]}
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"""
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handler = transport.factory.instance(**_args['store'])
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for cmd in _args['apply'] :
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handler.apply(cmd)
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handler.close()
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if __name__ == '__main__' :
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_info = json.loads(open (SYS_ARGS['config']).read())
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index = int(SYS_ARGS['index']) if 'index' in SYS_ARGS else None
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procs = []
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for _config in _info :
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if 'source' in SYS_ARGS :
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_config['source'] = {"type":"disk.DiskReader","args":{"path":SYS_ARGS['source'],"delimiter":","}}
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_config['jobs'] = 3 if 'jobs' not in SYS_ARGS else int(SYS_ARGS['jobs'])
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etl = ETL (**_config)
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if index is None:
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etl.start()
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procs.append(etl)
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elif _info.index(_config) == index :
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# print (_config)
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procs = [etl]
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etl.start()
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break
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#
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#
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N = len(procs)
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while procs :
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procs = [thread for thread in procs if not thread.is_done()]
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if len(procs) < N :
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print (["Finished ",(N-len(procs)), " remaining ", len(procs)])
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N = len(procs)
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time.sleep(1)
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print ("We're done !!")
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4
setup.py
4
setup.py
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@ -8,12 +8,12 @@ def read(fname):
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return open(os.path.join(os.path.dirname(__file__), fname)).read()
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args = {
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"name":"data-transport",
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"version":"1.4.6",
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"version":"1.4.8",
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"author":"The Phi Technology LLC","author_email":"info@the-phi.com",
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"license":"MIT",
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"packages":["transport"]}
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args["keywords"]=['mongodb','couchdb','rabbitmq','file','read','write','s3','sqlite']
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args["install_requires"] = ['pymongo','sqlalchemy','pandas','numpy','cloudant','pika','nzpy','boto3','boto','pyarrow','google-cloud-bigquery','google-cloud-bigquery-storage','flask-session','smart_open','botocore','psycopg2-binary','mysql-connector-python']
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args["install_requires"] = ['pymongo','sqlalchemy','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']
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args["url"] = "https://healthcareio.the-phi.com/git/code/transport.git"
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args['scripts'] = ['bin/transport']
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if sys.version_info[0] == 2 :
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@ -28,7 +28,7 @@ import importlib
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import sys
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import sqlalchemy
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if sys.version_info[0] > 2 :
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from transport.common import Reader, Writer #, factory
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from transport.common import Reader, Writer,Console #, factory
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from transport import disk
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from transport import s3 as s3
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@ -36,14 +36,16 @@ if sys.version_info[0] > 2 :
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from transport import couch as couch
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from transport import mongo as mongo
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from transport import sql as sql
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from transport import etl as etl
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else:
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from common import Reader, Writer #, factory
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from common import Reader, Writer,Console #, factory
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import disk
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import queue
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import couch
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import mongo
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import s3
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import sql
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import etl
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import psycopg2 as pg
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import mysql.connector as my
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from google.cloud import bigquery as bq
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@ -51,9 +53,12 @@ import nzpy as nz #--- netezza drivers
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import os
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class factory :
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TYPE = {"sql":{"providers":["postgresql","mysql","neteeza","bigquery","mariadb","redshift"]}}
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PROVIDERS = {
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"etl":{"class":{"read":etl.instance}},
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"console":{"class":{"write":Console,"read":Console}},
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"file":{"class":{"read":disk.DiskReader,"write":disk.DiskWriter}},
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"sqlite":{"class":{"read":disk.SQLiteReader,"write":disk.SQLiteWriter}},
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"postgresql":{"port":5432,"host":"localhost","database":os.environ['USER'],"driver":pg,"default":{"type":"VARCHAR"}},
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@ -140,8 +145,9 @@ def instance(**_args):
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#
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# Let us try to establish an sqlalchemy wrapper
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try:
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host = ''
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if provider not in ['bigquery','mongodb','couchdb','sqlite'] :
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if provider not in ['bigquery','mongodb','couchdb','sqlite','console','etl','file'] :
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#
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# In these cases we are assuming RDBMS and thus would exclude NoSQL and BigQuery
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username = args['username'] if 'username' in args else ''
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@ -159,7 +165,7 @@ def instance(**_args):
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account = ''
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host = ''
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database = args['path'] if 'path' in args else args['database']
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if provider not in ['mongodb','couchdb','bigquery'] :
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if provider not in ['mongodb','couchdb','bigquery','console','etl','file'] :
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uri = ''.join([provider,"://",account,host,'/',database])
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e = sqlalchemy.create_engine (uri,future=True)
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@ -21,6 +21,7 @@ __author__ = 'The Phi Technology'
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import numpy as np
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import json
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import importlib
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from multiprocessing import RLock
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# import couch
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# import mongo
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class IO:
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@ -89,6 +90,29 @@ class ReadWriter(Reader,Writer) :
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This class implements the read/write functions aggregated
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"""
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pass
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class Console(Writer):
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lock = RLock()
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def __init__(self,**_args):
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self.lock = _args['lock'] if 'lock' in _args else False
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self.info = self.write
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self.debug = self.write
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self.log = self.write
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pass
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def write (self,info,**_args):
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if self.lock :
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Console.lock.acquire()
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try:
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if type(info) == list:
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for row in info :
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print (row)
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else:
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print (info)
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except Exception as e :
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print (e)
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finally:
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if self.lock :
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Console.lock.release()
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# class factory :
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# @staticmethod
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# def instance(**args):
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@ -21,14 +21,17 @@ class DiskReader(Reader) :
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"""
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Reader.__init__(self)
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self.path = params['path'] ;
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self.path = params['path'] if 'path' in params else None
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self.delimiter = params['delimiter'] if 'delimiter' in params else ','
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def isready(self):
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return os.path.exists(self.path)
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def meta(self,**_args):
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return []
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def read(self,**args):
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_path = self.path if 'path' not in args else args['path']
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_delimiter = self.delimiter if 'delimiter' not in args else args['delimiter']
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return pd.read_csv(self.path,delimiter=self.delimiter)
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return pd.read_csv(_path,delimiter=self.delimiter)
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def stream(self,**args):
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"""
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This function reads the rows from a designated location on disk
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@ -84,15 +87,16 @@ class DiskWriter(Writer):
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self.cache['meta']['cols'] += len(row) if isinstance(row,list) else len(row.keys())
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self.cache['meta']['rows'] += 1
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return (self.delimiter.join(row) if self.delimiter else json.dumps(row))+"\n"
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def write(self,info):
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def write(self,info,**_args):
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"""
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This function writes a record to a designated file
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@param label <passed|broken|fixed|stats>
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@param row row to be written
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"""
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try:
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_mode = 'a' if 'overwrite' not in _args else 'w'
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DiskWriter.THREAD_LOCK.acquire()
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f = open(self.path,'a')
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f = open(self.path,_mode)
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if self.delimiter :
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if type(info) == list :
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for row in info :
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