From d438f69f02f4168a9a94ae0136fa402c38daa3bd Mon Sep 17 00:00:00 2001 From: Steve Nyemba Date: Tue, 17 Sep 2019 11:28:09 -0500 Subject: [PATCH] removed transport.py, old implementation --- transport.py | 758 --------------------------------------------------- 1 file changed, 758 deletions(-) delete mode 100755 transport.py diff --git a/transport.py b/transport.py deleted file mode 100755 index c6bd085..0000000 --- a/transport.py +++ /dev/null @@ -1,758 +0,0 @@ -""" - This file implements data transport stuctures in order to allow data to be moved to and from anywhere - We can thus read data from disk and write to the cloud,queue, or couchdb or SQL -""" -from flask import request, session -import os -import pika -import json -import numpy as np -from couchdbkit import Server -import re -from csv import reader -from datetime import datetime -import boto -import botocore -from smart_open import smart_open -""" - @TODO: Write a process by which the class automatically handles reading and creating a preliminary sample and discovers the meta data -""" -class Reader: - def __init__(self): - self.nrows = 0 - self.xchar = None - - def row_count(self): - content = self.read() - return np.sum([1 for row in content]) - """ - 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 - """ - def delimiter(self,sample): - - m = {',':[],'\t':[],'|':[],'\x3A':[]} - delim = m.keys() - for row in sample: - for xchar in delim: - if row.split(xchar) > 1: - m[xchar].append(len(row.split(xchar))) - else: - m[xchar].append(0) - - - - # - # The delimiter with the smallest variance, provided the mean is greater than 1 - # This would be troublesome if there many broken records sampled - # - m = {id: np.var(m[id]) for id in m.keys() if m[id] != [] and int(np.mean(m[id]))>1} - index = m.values().index( min(m.values())) - xchar = m.keys()[index] - - return xchar - """ - This function determines the number of columns of a given sample - @pre self.xchar is not None - """ - def col_count(self,sample): - - m = {} - i = 0 - - for row in sample: - row = self.format(row) - id = str(len(row)) - #id = str(len(row.split(self.xchar))) - - if id not in m: - m[id] = 0 - m[id] = m[id] + 1 - - index = m.values().index( max(m.values()) ) - ncols = int(m.keys()[index]) - - - return ncols; - """ - This function will clean records of a given row by removing non-ascii characters - @pre self.xchar is not None - """ - def format (self,row): - - if isinstance(row,list) == False: - # - # 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) - cols = self.split(row) - #cols = row.split(self.xchar) - else: - cols = row ; - return [ re.sub('[^\x00-\x7F,\n,\r,\v,\b,]',' ',col.strip()).strip().replace('"','') for col in cols] - - #if isinstance(row,list) == False: - # return (self.xchar.join(r)).format('utf-8') - #else: - # return r - """ - 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. - @pre : self.xchar is not None - """ - def split (self,row): - - pattern = "".join(["(?:^|",self.xchar,")(\"(?:[^\"]+|\"\")*\"|[^",self.xchar,"]*)"]) - return re.findall(pattern,row.replace('\n','')) - -class Writer: - - def format(self,row,xchar): - if xchar is not None and isinstance(row,list): - return xchar.join(row)+'\n' - elif xchar is None and isinstance(row,dict): - row = json.dumps(row) - return row - """ - It is important to be able to archive data so as to insure that growth is controlled - Nothing in nature grows indefinitely neither should data being handled. - """ - def archive(self): - pass - def flush(self): - pass - -""" - 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 - NOTE: This is inefficient and can crash a micro-instance (becareful) -""" -class HttpRequestReader(Reader): - def __init__(self,**params): - self.file_length = 0 - try: - - #self.file = params['file'] - #self.file.seek(0, os.SEEK_END) - #self.file_length = self.file.tell() - - #print 'size of file ',self.file_length - self.content = params['file'].readlines() - self.file_length = len(self.content) - except Exception, e: - print "Error ... ",e - pass - - def isready(self): - return self.file_length > 0 - def read(self,size =-1): - i = 1 - for row in self.content: - i += 1 - if size == i: - break - yield row - -""" - This class is designed to write data to a session/cookie -""" -class HttpSessionWriter(Writer): - """ - @param key required session key - """ - def __init__(self,**params): - 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'] - - - def format_sql(self,row): - values = "','".join([col.replace('"','').replace("'",'') for col in row]) - return "".join(["INSERT INTO :table VALUES('",values,"');\n"]).replace(':table',self.tablename) - def isready(self): - return True - def write(self,**params): - label = params['label'] - row = params ['row'] - - if label == 'usable': - self.session['csv'].append(self.format(row,',')) - self.session['sql'].append(self.format_sql(row)) - -""" - This class is designed to read data from disk (location on hard drive) - @pre : isready() == True -""" -class DiskReader(Reader) : - """ - @param path absolute path of the file to be read - """ - def __init__(self,**params): - Reader.__init__(self) - self.path = params['path'] ; - - def isready(self): - return os.path.exists(self.path) - """ - This function reads the rows from a designated location on disk - @param size number of rows to be read, -1 suggests all rows - """ - def read(self,size=-1): - f = open(self.path,'rU') - i = 1 - for row in f: - - i += 1 - if size == i: - break - yield row - f.close() -""" - This function writes output to disk in a designated location -""" -class DiskWriter(Writer): - def __init__(self,**params): - if 'path' in params: - self.path = params['path'] - else: - self.path = None - if 'name' in params: - self.name = params['name']; - else: - self.name = None - if os.path.exists(self.path) == False: - os.mkdir(self.path) - """ - This function determines if the class is ready for execution or not - i.e it determines if the preconditions of met prior execution - """ - def isready(self): - - p = self.path is not None and os.path.exists(self.path) - q = self.name is not None - return p and q - """ - This function writes a record to a designated file - @param label - @param row row to be written - """ - def write(self,**params): - label = params['label'] - row = params['row'] - xchar = None - if 'xchar' is not None: - xchar = params['xchar'] - path = ''.join([self.path,os.sep,label]) - if os.path.exists(path) == False: - os.mkdir(path) ; - path = ''.join([path,os.sep,self.name]) - f = open(path,'a') - row = self.format(row,xchar); - f.write(row) - f.close() -""" - This class hierarchy is designed to handle interactions with a queue server using pika framework (our tests are based on rabbitmq) -""" -class MessageQueue: - def __init__(self,**params): - self.host= params['host'] - self.uid = params['uid'] - self.qid = params['qid'] - - def isready(self): - #self.init() - resp = self.connection is not None and self.connection.is_open - self.close() - return resp - def close(self): - if self.connection.is_closed == False : - self.channel.close() - self.connection.close() -""" - This class is designed to publish content to an AMQP (Rabbitmq) - The class will rely on pika to implement this functionality - - We will publish information to a given queue for a given exchange -""" - -class QueueWriter(MessageQueue,Writer): - def __init__(self,**params): - #self.host= params['host'] - #self.uid = params['uid'] - #self.qid = params['queue'] - MessageQueue.__init__(self,**params); - - - def init(self,label=None): - properties = pika.ConnectionParameters(host=self.host) - self.connection = pika.BlockingConnection(properties) - self.channel = self.connection.channel() - self.info = self.channel.exchange_declare(exchange=self.uid,type='direct',durable=True) - if label is None: - self.qhandler = self.channel.queue_declare(queue=self.qid,durable=True) - else: - self.qhandler = self.channel.queue_declare(queue=label,durable=True) - - self.channel.queue_bind(exchange=self.uid,queue=self.qhandler.method.queue) - - - - """ - This function writes a stream of data to the a given queue - @param object object to be written (will be converted to JSON) - @TODO: make this less chatty - """ - def write(self,**params): - xchar = None - if 'xchar' in params: - xchar = params['xchar'] - object = self.format(params['row'],xchar) - - label = params['label'] - self.init(label) - _mode = 2 - if isinstance(object,str): - stream = object - _type = 'text/plain' - else: - stream = json.dumps(object) - if 'type' in params : - _type = params['type'] - else: - _type = 'application/json' - - self.channel.basic_publish( - exchange=self.uid, - routing_key=label, - body=stream, - properties=pika.BasicProperties(content_type=_type,delivery_mode=_mode) - ); - self.close() - - def flush(self,label): - self.init(label) - _mode = 1 #-- Non persistent - self.channel.queue_delete( queue=label); - self.close() - -""" - This class will read from a queue provided an exchange, queue and host - @TODO: Account for security and virtualhosts -""" -class QueueReader(MessageQueue,Reader): - """ - @param host host - @param uid exchange identifier - @param qid queue identifier - """ - def __init__(self,**params): - #self.host= params['host'] - #self.uid = params['uid'] - #self.qid = params['qid'] - MessageQueue.__init__(self,**params); - if 'durable' in params : - self.durable = True - else: - self.durable = False - self.size = -1 - self.data = {} - def init(self,qid): - - properties = pika.ConnectionParameters(host=self.host) - self.connection = pika.BlockingConnection(properties) - self.channel = self.connection.channel() - self.channel.exchange_declare(exchange=self.uid,type='direct',durable=True) - - self.info = self.channel.queue_declare(queue=qid,durable=True) - - - - """ - This is the callback function designed to process the data stream from the queue - - """ - def callback(self,channel,method,header,stream): - - r = [] - if re.match("^\{|\[",stream) is not None: - r = json.loads(stream) - else: - - r = stream - - qid = self.info.method.queue - if qid not in self.data : - self.data[qid] = [] - - self.data[qid].append(r) - # - # We stop reading when the all the messages of the queue are staked - # - if self.size == len(self.data[qid]) or len(self.data[qid]) == self.info.method.message_count: - self.close() - - """ - This function will read, the first message from a queue - @TODO: - Implement channel.basic_get in order to retrieve a single message at a time - Have the number of messages retrieved be specified by size (parameter) - """ - def read(self,size=-1): - r = {} - self.size = size - # - # We enabled the reader to be able to read from several queues (sequentially for now) - # The qid parameter will be an array of queues the reader will be reading from - # - if isinstance(self.qid,basestring) : - self.qid = [self.qid] - for qid in self.qid: - self.init(qid) - # r[qid] = [] - - if self.info.method.message_count > 0: - - self.channel.basic_consume(self.callback,queue=qid,no_ack=False); - self.channel.start_consuming() - else: - - pass - #self.close() - # r[qid].append( self.data) - - return self.data -class QueueListener(QueueReader): - def init(self,qid): - properties = pika.ConnectionParameters(host=self.host) - self.connection = pika.BlockingConnection(properties) - self.channel = self.connection.channel() - self.channel.exchange_declare(exchange=self.uid,type='direct',durable=True ) - - self.info = self.channel.queue_declare(passive=True,exclusive=True,queue=qid) - - self.channel.queue_bind(exchange=self.uid,queue=self.info.method.queue,routing_key=qid) - #self.callback = callback - def read(self): - - self.init(self.qid) - self.channel.basic_consume(self.callback,queue=self.qid,no_ack=True); - self.channel.start_consuming() - -""" - This class is designed to write output as sql insert statements - The class will inherit from DiskWriter with minor adjustments - @TODO: Include script to create the table if need be using the upper bound of a learner -""" -class SQLDiskWriter(DiskWriter): - def __init__(self,**args): - DiskWriter.__init__(self,**args) - self.tablename = re.sub('\..+$','',self.name).replace(' ','_') - """ - @param label - @param row - @param xchar - """ - def write(self,**args): - label = args['label'] - row = args['row'] - - if label == 'usable': - values = "','".join([col.replace('"','').replace("'",'') for col in row]) - row = "".join(["INSERT INTO :table VALUES('",values,"');\n"]).replace(':table',self.tablename) - - args['row'] = row - DiskWriter.write(self,**args) -class Couchdb: - """ - @param uri host & port reference - @param uid user id involved - - @param dbname database name (target) - """ - def __init__(self,**args): - uri = args['uri'] - self.uid = args['uid'] - dbname = args['dbname'] - self.server = Server(uri=uri) - self.dbase = self.server.get_db(dbname) - if self.dbase.doc_exist(self.uid) == False: - self.dbase.save_doc({"_id":self.uid}) - """ - Insuring the preconditions are met for processing - """ - def isready(self): - p = self.server.info() != {} - if p == False or self.dbase.dbname not in self.server.all_dbs(): - return False - # - # At this point we are sure that the server is connected - # We are also sure that the database actually exists - # - q = self.dbase.doc_exist(self.uid) - if q == False: - return False - return True - def view(self,id,**args): - r =self.dbase.view(id,**args) - r = r.all() - return r[0]['value'] if len(r) > 0 else [] - -""" - This function will read an attachment from couchdb and return it to calling code. The attachment must have been placed before hand (otherwise oops) - @T: Account for security & access control -""" -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')