removed transport.py, old implementation
This commit is contained in:
Steve Nyemba
parent
e8328e577d
commit
d438f69f02
758
transport.py
758
transport.py
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@ -1,758 +0,0 @@
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"""
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This file implements data transport stuctures in order to allow data to be moved to and from anywhere
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We can thus read data from disk and write to the cloud,queue, or couchdb or SQL
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"""
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from flask import request, session
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import os
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import pika
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import json
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import numpy as np
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from couchdbkit import Server
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import re
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from csv import reader
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from datetime import datetime
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import boto
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import botocore
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from smart_open import smart_open
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"""
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@TODO: Write a process by which the class automatically handles reading and creating a preliminary sample and discovers the meta data
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"""
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class Reader:
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def __init__(self):
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self.nrows = 0
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self.xchar = None
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def row_count(self):
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content = self.read()
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return np.sum([1 for row in content])
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"""
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This function determines the most common delimiter from a subset of possible delimiters. It uses a statistical approach to guage the distribution of columns for a given delimiter
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"""
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def delimiter(self,sample):
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m = {',':[],'\t':[],'|':[],'\x3A':[]}
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delim = m.keys()
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for row in sample:
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for xchar in delim:
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if row.split(xchar) > 1:
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m[xchar].append(len(row.split(xchar)))
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else:
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m[xchar].append(0)
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#
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# The delimiter with the smallest variance, provided the mean is greater than 1
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# This would be troublesome if there many broken records sampled
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#
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m = {id: np.var(m[id]) for id in m.keys() if m[id] != [] and int(np.mean(m[id]))>1}
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index = m.values().index( min(m.values()))
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xchar = m.keys()[index]
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return xchar
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"""
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This function determines the number of columns of a given sample
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@pre self.xchar is not None
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"""
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def col_count(self,sample):
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m = {}
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i = 0
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for row in sample:
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row = self.format(row)
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id = str(len(row))
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#id = str(len(row.split(self.xchar)))
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if id not in m:
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m[id] = 0
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m[id] = m[id] + 1
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index = m.values().index( max(m.values()) )
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ncols = int(m.keys()[index])
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return ncols;
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"""
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This function will clean records of a given row by removing non-ascii characters
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@pre self.xchar is not None
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"""
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def format (self,row):
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if isinstance(row,list) == False:
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#
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# We've observed sometimes fields contain delimiter as a legitimate character, we need to be able to account for this and not tamper with the field values (unless necessary)
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cols = self.split(row)
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#cols = row.split(self.xchar)
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else:
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cols = row ;
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return [ re.sub('[^\x00-\x7F,\n,\r,\v,\b,]',' ',col.strip()).strip().replace('"','') for col in cols]
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#if isinstance(row,list) == False:
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# return (self.xchar.join(r)).format('utf-8')
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#else:
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# return r
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"""
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This function performs a split of a record and tries to attempt to preserve the integrity of the data within i.e accounting for the double quotes.
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@pre : self.xchar is not None
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"""
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def split (self,row):
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pattern = "".join(["(?:^|",self.xchar,")(\"(?:[^\"]+|\"\")*\"|[^",self.xchar,"]*)"])
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return re.findall(pattern,row.replace('\n',''))
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class Writer:
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def format(self,row,xchar):
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if xchar is not None and isinstance(row,list):
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return xchar.join(row)+'\n'
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elif xchar is None and isinstance(row,dict):
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row = json.dumps(row)
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return row
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"""
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It is important to be able to archive data so as to insure that growth is controlled
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Nothing in nature grows indefinitely neither should data being handled.
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"""
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def archive(self):
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pass
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def flush(self):
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pass
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"""
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This class is designed to read data from an Http request file handler provided to us by flask
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The file will be heald in memory and processed accordingly
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NOTE: This is inefficient and can crash a micro-instance (becareful)
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"""
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class HttpRequestReader(Reader):
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def __init__(self,**params):
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self.file_length = 0
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try:
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#self.file = params['file']
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#self.file.seek(0, os.SEEK_END)
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#self.file_length = self.file.tell()
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#print 'size of file ',self.file_length
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self.content = params['file'].readlines()
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self.file_length = len(self.content)
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except Exception, e:
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print "Error ... ",e
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pass
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def isready(self):
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return self.file_length > 0
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def read(self,size =-1):
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i = 1
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for row in self.content:
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i += 1
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if size == i:
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break
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yield row
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"""
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This class is designed to write data to a session/cookie
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"""
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class HttpSessionWriter(Writer):
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"""
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@param key required session key
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"""
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def __init__(self,**params):
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self.session = params['queue']
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self.session['sql'] = []
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self.session['csv'] = []
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self.tablename = re.sub('..+$','',params['filename'])
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self.session['uid'] = params['uid']
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#self.xchar = params['xchar']
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def format_sql(self,row):
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values = "','".join([col.replace('"','').replace("'",'') for col in row])
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return "".join(["INSERT INTO :table VALUES('",values,"');\n"]).replace(':table',self.tablename)
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def isready(self):
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return True
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def write(self,**params):
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label = params['label']
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row = params ['row']
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if label == 'usable':
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self.session['csv'].append(self.format(row,','))
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self.session['sql'].append(self.format_sql(row))
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"""
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This class is designed to read data from disk (location on hard drive)
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@pre : isready() == True
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"""
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class DiskReader(Reader) :
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"""
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@param path absolute path of the file to be read
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"""
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def __init__(self,**params):
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Reader.__init__(self)
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self.path = params['path'] ;
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def isready(self):
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return os.path.exists(self.path)
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"""
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This function reads the rows from a designated location on disk
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@param size number of rows to be read, -1 suggests all rows
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"""
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def read(self,size=-1):
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f = open(self.path,'rU')
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i = 1
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for row in f:
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i += 1
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if size == i:
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break
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yield row
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f.close()
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"""
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This function writes output to disk in a designated location
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"""
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class DiskWriter(Writer):
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def __init__(self,**params):
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if 'path' in params:
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self.path = params['path']
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else:
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self.path = None
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if 'name' in params:
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self.name = params['name'];
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else:
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self.name = None
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if os.path.exists(self.path) == False:
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os.mkdir(self.path)
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"""
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This function determines if the class is ready for execution or not
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i.e it determines if the preconditions of met prior execution
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"""
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def isready(self):
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p = self.path is not None and os.path.exists(self.path)
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q = self.name is not None
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return p and q
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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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def write(self,**params):
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label = params['label']
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row = params['row']
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xchar = None
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if 'xchar' is not None:
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xchar = params['xchar']
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path = ''.join([self.path,os.sep,label])
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if os.path.exists(path) == False:
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os.mkdir(path) ;
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path = ''.join([path,os.sep,self.name])
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f = open(path,'a')
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row = self.format(row,xchar);
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f.write(row)
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f.close()
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"""
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This class hierarchy is designed to handle interactions with a queue server using pika framework (our tests are based on rabbitmq)
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"""
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class MessageQueue:
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def __init__(self,**params):
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self.host= params['host']
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self.uid = params['uid']
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self.qid = params['qid']
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def isready(self):
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#self.init()
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resp = self.connection is not None and self.connection.is_open
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self.close()
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return resp
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def close(self):
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if self.connection.is_closed == False :
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self.channel.close()
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self.connection.close()
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"""
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This class is designed to publish content to an AMQP (Rabbitmq)
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The class will rely on pika to implement this functionality
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We will publish information to a given queue for a given exchange
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"""
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class QueueWriter(MessageQueue,Writer):
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def __init__(self,**params):
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#self.host= params['host']
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#self.uid = params['uid']
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#self.qid = params['queue']
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MessageQueue.__init__(self,**params);
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def init(self,label=None):
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properties = pika.ConnectionParameters(host=self.host)
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self.connection = pika.BlockingConnection(properties)
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self.channel = self.connection.channel()
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self.info = self.channel.exchange_declare(exchange=self.uid,type='direct',durable=True)
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if label is None:
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self.qhandler = self.channel.queue_declare(queue=self.qid,durable=True)
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else:
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self.qhandler = self.channel.queue_declare(queue=label,durable=True)
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self.channel.queue_bind(exchange=self.uid,queue=self.qhandler.method.queue)
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"""
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This function writes a stream of data to the a given queue
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@param object object to be written (will be converted to JSON)
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@TODO: make this less chatty
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"""
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def write(self,**params):
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xchar = None
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if 'xchar' in params:
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xchar = params['xchar']
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object = self.format(params['row'],xchar)
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label = params['label']
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self.init(label)
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_mode = 2
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if isinstance(object,str):
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stream = object
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_type = 'text/plain'
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else:
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stream = json.dumps(object)
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if 'type' in params :
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_type = params['type']
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else:
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_type = 'application/json'
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self.channel.basic_publish(
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exchange=self.uid,
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routing_key=label,
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body=stream,
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properties=pika.BasicProperties(content_type=_type,delivery_mode=_mode)
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);
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self.close()
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def flush(self,label):
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self.init(label)
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_mode = 1 #-- Non persistent
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self.channel.queue_delete( queue=label);
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self.close()
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"""
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This class will read from a queue provided an exchange, queue and host
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@TODO: Account for security and virtualhosts
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"""
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class QueueReader(MessageQueue,Reader):
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"""
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@param host host
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@param uid exchange identifier
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@param qid queue identifier
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"""
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def __init__(self,**params):
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#self.host= params['host']
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#self.uid = params['uid']
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#self.qid = params['qid']
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MessageQueue.__init__(self,**params);
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if 'durable' in params :
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self.durable = True
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else:
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self.durable = False
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self.size = -1
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self.data = {}
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def init(self,qid):
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properties = pika.ConnectionParameters(host=self.host)
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self.connection = pika.BlockingConnection(properties)
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self.channel = self.connection.channel()
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self.channel.exchange_declare(exchange=self.uid,type='direct',durable=True)
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self.info = self.channel.queue_declare(queue=qid,durable=True)
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"""
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This is the callback function designed to process the data stream from the queue
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"""
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def callback(self,channel,method,header,stream):
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r = []
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if re.match("^\{|\[",stream) is not None:
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r = json.loads(stream)
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else:
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r = stream
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qid = self.info.method.queue
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if qid not in self.data :
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self.data[qid] = []
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self.data[qid].append(r)
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#
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# We stop reading when the all the messages of the queue are staked
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#
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if self.size == len(self.data[qid]) or len(self.data[qid]) == self.info.method.message_count:
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self.close()
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"""
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This function will read, the first message from a queue
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@TODO:
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Implement channel.basic_get in order to retrieve a single message at a time
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Have the number of messages retrieved be specified by size (parameter)
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"""
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def read(self,size=-1):
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r = {}
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self.size = size
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#
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# We enabled the reader to be able to read from several queues (sequentially for now)
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# The qid parameter will be an array of queues the reader will be reading from
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#
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if isinstance(self.qid,basestring) :
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self.qid = [self.qid]
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for qid in self.qid:
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self.init(qid)
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# r[qid] = []
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if self.info.method.message_count > 0:
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self.channel.basic_consume(self.callback,queue=qid,no_ack=False);
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self.channel.start_consuming()
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else:
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pass
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#self.close()
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# r[qid].append( self.data)
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return self.data
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class QueueListener(QueueReader):
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def init(self,qid):
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properties = pika.ConnectionParameters(host=self.host)
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self.connection = pika.BlockingConnection(properties)
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self.channel = self.connection.channel()
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self.channel.exchange_declare(exchange=self.uid,type='direct',durable=True )
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self.info = self.channel.queue_declare(passive=True,exclusive=True,queue=qid)
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self.channel.queue_bind(exchange=self.uid,queue=self.info.method.queue,routing_key=qid)
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#self.callback = callback
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def read(self):
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self.init(self.qid)
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self.channel.basic_consume(self.callback,queue=self.qid,no_ack=True);
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self.channel.start_consuming()
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"""
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This class is designed to write output as sql insert statements
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The class will inherit from DiskWriter with minor adjustments
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@TODO: Include script to create the table if need be using the upper bound of a learner
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"""
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class SQLDiskWriter(DiskWriter):
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def __init__(self,**args):
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DiskWriter.__init__(self,**args)
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self.tablename = re.sub('\..+$','',self.name).replace(' ','_')
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"""
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@param label
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@param row
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@param xchar
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"""
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def write(self,**args):
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label = args['label']
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row = args['row']
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if label == 'usable':
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values = "','".join([col.replace('"','').replace("'",'') for col in row])
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row = "".join(["INSERT INTO :table VALUES('",values,"');\n"]).replace(':table',self.tablename)
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args['row'] = row
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DiskWriter.write(self,**args)
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class Couchdb:
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"""
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@param uri host & port reference
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@param uid user id involved
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@param dbname database name (target)
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"""
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def __init__(self,**args):
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uri = args['uri']
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self.uid = args['uid']
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dbname = args['dbname']
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self.server = Server(uri=uri)
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self.dbase = self.server.get_db(dbname)
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if self.dbase.doc_exist(self.uid) == False:
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self.dbase.save_doc({"_id":self.uid})
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"""
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Insuring the preconditions are met for processing
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"""
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def isready(self):
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p = self.server.info() != {}
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if p == False or self.dbase.dbname not in self.server.all_dbs():
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return False
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#
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# At this point we are sure that the server is connected
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# We are also sure that the database actually exists
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#
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q = self.dbase.doc_exist(self.uid)
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if q == False:
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return False
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return True
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def view(self,id,**args):
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r =self.dbase.view(id,**args)
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r = r.all()
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return r[0]['value'] if len(r) > 0 else []
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"""
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This function will read an attachment from couchdb and return it to calling code. The attachment must have been placed before hand (otherwise oops)
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@T: Account for security & access control
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"""
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class CouchdbReader(Couchdb,Reader):
|
||||
"""
|
||||
@param filename filename (attachment)
|
||||
"""
|
||||
def __init__(self,**args):
|
||||
#
|
||||
# setting the basic parameters for
|
||||
Couchdb.__init__(self,**args)
|
||||
if 'filename' in args :
|
||||
self.filename = args['filename']
|
||||
else:
|
||||
self.filename = None
|
||||
|
||||
def isready(self):
|
||||
#
|
||||
# Is the basic information about the database valid
|
||||
#
|
||||
p = Couchdb.isready(self)
|
||||
|
||||
if p == False:
|
||||
return False
|
||||
#
|
||||
# The database name is set and correct at this point
|
||||
# We insure the document of the given user has the requested attachment.
|
||||
#
|
||||
|
||||
doc = self.dbase.get(self.uid)
|
||||
|
||||
if '_attachments' in doc:
|
||||
r = self.filename in doc['_attachments'].keys()
|
||||
|
||||
else:
|
||||
r = False
|
||||
|
||||
return r
|
||||
def stream(self):
|
||||
content = self.dbase.fetch_attachment(self.uid,self.filename).split('\n') ;
|
||||
i = 1
|
||||
for row in content:
|
||||
yield row
|
||||
if size > 0 and i == size:
|
||||
break
|
||||
i = i + 1
|
||||
|
||||
def read(self,size=-1):
|
||||
if self.filename is not None:
|
||||
self.stream()
|
||||
else:
|
||||
return self.basic_read()
|
||||
def basic_read(self):
|
||||
document = self.dbase.get(self.uid)
|
||||
del document['_id'], document['_rev']
|
||||
return document
|
||||
"""
|
||||
This class will write on a couchdb document provided a scope
|
||||
The scope is the attribute that will be on the couchdb document
|
||||
"""
|
||||
class CouchdbWriter(Couchdb,Writer):
|
||||
"""
|
||||
@param uri host & port reference
|
||||
@param uid user id involved
|
||||
@param filename filename (attachment)
|
||||
@param dbname database name (target)
|
||||
"""
|
||||
def __init__(self,**args):
|
||||
|
||||
Couchdb.__init__(self,**args)
|
||||
uri = args['uri']
|
||||
self.uid = args['uid']
|
||||
if 'filename' in args:
|
||||
self.filename = args['filename']
|
||||
else:
|
||||
self.filename = None
|
||||
dbname = args['dbname']
|
||||
self.server = Server(uri=uri)
|
||||
self.dbase = self.server.get_db(dbname)
|
||||
#
|
||||
# If the document doesn't exist then we should create it
|
||||
#
|
||||
|
||||
"""
|
||||
write a given attribute to a document database
|
||||
@param label scope of the row repair|broken|fixed|stats
|
||||
@param row row to be written
|
||||
"""
|
||||
def write(self,**params):
|
||||
|
||||
document = self.dbase.get(self.uid)
|
||||
label = params['label']
|
||||
row = params['row']
|
||||
if label not in document :
|
||||
document[label] = []
|
||||
document[label].append(row)
|
||||
self.dbase.save_doc(document)
|
||||
def flush(self,**params) :
|
||||
|
||||
size = params['size'] if 'size' in params else 0
|
||||
has_changed = False
|
||||
document = self.dbase.get(self.uid)
|
||||
for key in document:
|
||||
if key not in ['_id','_rev','_attachments'] :
|
||||
content = document[key]
|
||||
else:
|
||||
continue
|
||||
if isinstance(content,list) and size > 0:
|
||||
index = len(content) - size
|
||||
content = content[index:]
|
||||
document[key] = content
|
||||
|
||||
else:
|
||||
document[key] = {}
|
||||
has_changed = True
|
||||
|
||||
self.dbase.save_doc(document)
|
||||
|
||||
def archive(self,params=None):
|
||||
document = self.dbase.get(self.uid)
|
||||
content = {}
|
||||
_doc = {}
|
||||
for id in document:
|
||||
if id in ['_id','_rev','_attachments'] :
|
||||
_doc[id] = document[id]
|
||||
else:
|
||||
content[id] = document[id]
|
||||
|
||||
content = json.dumps(content)
|
||||
document= _doc
|
||||
now = str(datetime.today())
|
||||
|
||||
name = '-'.join([document['_id'] , now,'.json'])
|
||||
self.dbase.save_doc(document)
|
||||
self.dbase.put_attachment(document,content,name,'application/json')
|
||||
class s3 :
|
||||
"""
|
||||
@TODO: Implement a search function for a file given a bucket??
|
||||
"""
|
||||
def __init__(self,args) :
|
||||
"""
|
||||
This function will extract a file or set of files from s3 bucket provided
|
||||
@param access_key
|
||||
@param secret_key
|
||||
@param path location of the file
|
||||
@param filter filename or filtering elements
|
||||
"""
|
||||
try:
|
||||
self.s3 = boto.connect_s3(args['access_key'],args['secret_key'])
|
||||
self.bucket = self.s3.get_bucket(args['bucket'].strip(),validate=False) if 'bucket' in args else None
|
||||
# self.path = args['path']
|
||||
self.filter = args['filter'] if 'filter' in args else None
|
||||
self.filename = args['file'] if 'file' in args else None
|
||||
|
||||
except Exception as e :
|
||||
self.s3 = None
|
||||
self.bucket = None
|
||||
print e
|
||||
def buckets(self):
|
||||
"""
|
||||
This function is a wrapper around the bucket list of buckets for s3
|
||||
|
||||
"""
|
||||
return self.s3.get_all_buckets()
|
||||
|
||||
|
||||
class s3Reader(s3,Reader) :
|
||||
"""
|
||||
Because s3 contains buckets and files, reading becomes a tricky proposition :
|
||||
- list files if file is None
|
||||
- stream content if file is Not None
|
||||
@TODO: support read from all buckets, think about it
|
||||
"""
|
||||
def __init__(self,args) :
|
||||
s3.__init__(self,args)
|
||||
def files(self):
|
||||
r = []
|
||||
try:
|
||||
return [item.name for item in self.bucket if item.size > 0]
|
||||
except Exception as e:
|
||||
pass
|
||||
return r
|
||||
def stream(self,limit=-1):
|
||||
"""
|
||||
At this point we should stream a file from a given bucket
|
||||
"""
|
||||
key = self.bucket.get_key(self.filename.strip())
|
||||
if key is None :
|
||||
yield None
|
||||
else:
|
||||
count = 0
|
||||
with smart_open(key) as remote_file:
|
||||
for line in remote_file:
|
||||
if count == limit and limit > 0 :
|
||||
break
|
||||
yield line
|
||||
count += 1
|
||||
def read(self,limit=-1) :
|
||||
if self.filename is None :
|
||||
#
|
||||
# returning the list of files because no one file was specified.
|
||||
return self.files()
|
||||
else:
|
||||
return self.stream(10)
|
||||
"""
|
||||
This class acts as a factory to be able to generate an instance of a Reader/Writer
|
||||
Against a Queue,Disk,Cloud,Couchdb
|
||||
The class doesn't enforce parameter validation, thus any error with the parameters sent will result in a null Object
|
||||
"""
|
||||
class Factory:
|
||||
def instance(self,**args):
|
||||
source = args['type']
|
||||
params = args['args']
|
||||
anObject = None
|
||||
|
||||
if source in ['HttpRequestReader','HttpSessionWriter']:
|
||||
#
|
||||
# @TODO: Make sure objects are serializable, be smart about them !!
|
||||
#
|
||||
aClassName = ''.join([source,'(**params)'])
|
||||
|
||||
|
||||
else:
|
||||
|
||||
stream = json.dumps(params)
|
||||
aClassName = ''.join([source,'(**',stream,')'])
|
||||
try:
|
||||
|
||||
|
||||
anObject = eval( aClassName)
|
||||
#setattr(anObject,'name',source)
|
||||
except Exception,e:
|
||||
print ['Error ',e]
|
||||
return anObject
|
||||
class s3Writer(s3,Writer) :
|
||||
def __init__(self,args) :
|
||||
s3.__init__(self,args)
|
||||
|
||||
"""
|
||||
This class implements a data-source handler that is intended to be used within the context of data processing, it allows to read/write anywhere transparently.
|
||||
The class is a facade to a heterogeneous class hierarchy and thus simplifies how the calling code interacts with the class hierarchy
|
||||
"""
|
||||
class DataSource:
|
||||
def __init__(self,sourceType='Disk',outputType='Disk',params={}):
|
||||
self.Input = DataSourceFactory.instance(type=sourceType,args=params)
|
||||
self.Output= DataSourceFactory.instance(type=outputType,args=params)
|
||||
def read(self,size=-1):
|
||||
return self.Input.read(size)
|
||||
def write(self,**args):
|
||||
self.Output.write(**args)
|
||||
conf = json.loads(open('config.json').read())
|
||||
#x = s3Reader( dict(conf,**{'bucket':'com.phi.sample.data','file':'Sample-Spreadsheet-5000-rows.csv'}))
|
||||
x = s3Reader(conf)
|
||||
print conf
|
||||
print x.bucket.get_all_keys()
|
||||
# r = x.read()
|
||||
# for item in r :
|
||||
# print item
|
||||
#print buckets[1].get_key('Sample-Spreadsheet-5000-rows.csv')
|
||||
Loading…
Reference in New Issue