parser/healthcareio/export/workers.py

"""
    HealthcareIO - The Phi Technology LLC 2020

    This file contains functionalities that implement elements of an ETL pipeline that will consist of various workers. 
    The pipeline is built around an observer design pattern.
    
    @TODO: Integrate with airflow and other process monitoring tools
"""
import transport
import os
from multiprocessing import Process
import numpy as np
import json
class Subject (Process):
    def __init__(self,**_args):
        super().__init__()
        self.observers = _args['observers']
        self.index = 0
        self.name = _args['name']
        self.table = self.observers[1].table
        pass
    def run(self):        
        self.notify()
    def notify(self):
        if self.index < len(self.observers) :
            observer = self.observers[self.index]             
            _observer = None if self.index == 0 else self.observers[self.index -1]
            _invalues = None if not _observer else _observer.get()
            observer.init(caller=self,invalues = _invalues)        
            self.index += 1            
            observer.execute()
        
class Worker :
    def __init__(self,**_args):
        #PATH = os.sep.join([os.environ['HOME'],'.healthcareio','config.json'])
        #CONFIG = json.loads((open(PATH)).read())
        self._info = _args['store']
        self.logs = []
        self.schema = _args['schema']
        self.prefix = _args['prefix']
        
    def name(self):
        return self.__class__.__name__ 
    def log (self,**_args):
        """
        This function is designed to log to either the console or a data-store
        """
        print (_args)
        pass
    def init(self,**_args):
        """
        Initializing a worker with arguments needed for it to perform it's task basic information needed are
        :param caller   caller to be notified
        :param store    data-store information i.e (pgsql,couchdb, mongo ...)
        """
        self.caller = _args['caller']
        #self._info      = _args['store']
        self._invalues  = _args['invalues'] if 'invalues' in _args else None
    def execute(self):
        try:
            self._apply()
        except Exception as error:
            print ()
            print (error)
            print ()
        finally:
            
            self.caller.notify() 
    def _apply(self):        
        pass
    def get(self):
        pass
    def notify(self):
        self.caller.notify()
    def tablename(self,name) :
        PREFIX_SEPARATOR = '_' if '_' not in self.prefix else ''
        SCHEMA_SEPARATOR = '' if self.schema.strip() =='' else '.'
        TABLE_NAME =  PREFIX_SEPARATOR.join([self.prefix,name]) 
        return SCHEMA_SEPARATOR.join([self.schema,TABLE_NAME])
        

class CreateSQL(Worker) :
    """
    This class is intended to create an SQL Table given the 
    """
    def __init__(self,**_args):
        super().__init__(**_args)
        self._sql = _args['sql']
    def init(self,**_args):
        super().init(**_args)
    
    def _apply(self) :
        
        sqltable = self.tablename(self._info['args']['table'])
        # log = {"context":self.name(),"args":{"table":self._info['args']['table'],"sql":self._sql}}
        log = {"context":self.name(),"args":{"table":sqltable,"sql":self._sql.replace(":table",sqltable)}}
        try:
           
            
            writer  = transport.factory.instance(**self._info)            
            writer.apply(self._sql.replace(":table",sqltable))
            writer.close()
            log['status'] = 1
        except Exception as e:
            log['status'] = 0
            log['info']  = {"error":e.args[0]}
            print (e)
        finally:
            self.log(**log)

class Reader(Worker):
    """
    read from mongodb and and make the data available to a third party
    :param pipeline mongodb command
    :param max_rows maximum rows to be written in a single insert
    """
    def __init__(self,**_args):
        super().__init__(**_args) 
    
        
        self.pipeline = _args['mongo']  #-- pipeline in the context of mongodb NOT ETL
        self.MAX_ROWS = _args['max_rows']
        self.table = _args['table']
        
        # is_demo = 'features' not in _args or ('features' in _args and ('export_etl' not in _args['features'] or _args['features']['export_etl'] == 0))        
        #
        # @TODO: Bundle the limits with the features so as to insure that it doesn't come across as a magic number
        #
        # LIMIT = -1
        # if is_demo :
        #     LIMIT = 10000
        #     if set(['find','distinct']) & set(self.pipeline.keys()) :
        #         self.pipeline['limit'] = LIMIT
        #     elif 'aggregate' in self.pipeline :
                
        #         self.pipeline['pipeline'] = [{"$limit":LIMIT}] + self.pipeline['pipeline']
        #     self.log(**{"context":self.name(),"demo":is_demo,"args":{"limit":LIMIT}})
    
    def init(self,**_args):
        super().init(**_args)
        self.rows = []
  
    def _apply(self):
        self.reader = transport.factory.instance(**self._info) ; 
        print()
        print (self.table)
        print (json.dumps(self.pipeline))
        print ()
        self.rows = self.reader.read(mongo=self.pipeline)

        N = len(self.rows) / self.MAX_ROWS  if len(self.rows) > self.MAX_ROWS else 1
        N = int(N) 
        # self.rows = rows
        _log = {"context":self.name(),"args":self._info['args']['db'], "status":1,"info":{"rows":len(self.rows),"table":self.table,"segments":N}}
        self.rows  = np.array_split(self.rows,N)

        
        # self.get = lambda : rows #np.array_split(rows,N)
        self.reader.close()
        
        #
        self.log(**_log)
        # @TODO: Call the caller and notify it that this here is done
    def get(self):       
        return self.rows
        

class Writer(Worker):
    def __init__(self,**_args):
        super().__init__(**_args)
    def init(self,**_args):
        """
        :param  store   output data-store needed for writing
        :param invalues input values with to be written somewhere
        """
        super().init(**_args)
        
        self._invalues = _args['invalues']
        
    def _apply(self):
        
        # table = self._info['args']['table'] if 'table' in self._info['args'] else 'N/A'
        table = self.tablename(self._info['args']['table'])
        
        self._info['args']['table'] = table;
        writer = transport.factory.instance(**self._info) 
        index = 0
        
        if self._invalues :
            for rows in self._invalues :
                # print (['segment # ',index,len(rows)])
                self.log(**{"context":self.name(),"segment":(index+1),"args":{"rows":len(rows),"table":table}})                
                if len(rows) :
                    #
                    # @TODO: Upgrade to mongodb 4.0+ and remove the line below 
                    # Upon upgrade use the operator "$toString" in export.init function
                    #
                    rows = [dict(item,**{"_id":str(item["_id"])}) for item in rows]
                    writer.write(rows)
                index += 1
                # for _e in rows :
                    # writer.write(_e) 

                
                
        else:
            print ("No data was passed")
        
            
        writer.close()

#_args = {"type":"mongo.MongoReader","args":{"db":"parserio","doc":"logs"}} 
#reader = Reader()
#reader.init(store = _args,pipeline={"distinct":"claims","key":"name"})
#reader._apply()
#print (reader.get())
#for row in reader.get() :
#    print (row)