cdplib/cdplib/db_handlers/MongodbHandler.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-

"""
Created on Mon Sep 16 13:27:44 2019

@author: oskar
@description: Implementation of a database handler for abstraction of the mongodb.
"""



import simplejson
import sys
import os
import time

import pymongo
from pymongo import MongoClient
import pandas as pd
import numpy as np
from pprint import pprint

sys.path.append(os.getcwd())
from cdplib.log import Log
from cdplib.db_migration.ParseJsonSchema import ParseJsonSchema
from cdplib.Singleton_Threadsafe import SingletonThreadsafe

class MongodbHandlerPool(metaclass=SingletonThreadsafe):
#class MongodbHandlerPool():
    '''
    '''

    def __init__(self, size: int = 1):
        self._size = size
        self._mongodb_handlers = [MongodbHandler() for _ in range(size)]

    def aquire(self):
        while not self._mongodb_handlers:
            self._mongodb_handlers = [MongodbHandler() for _ in range(self._size)]
            log.warning("Ran out of Mongodb handlers, 10 more have been added. Are you sure you've returned yours?")
        return self._mongodb_handlers.pop()

    def release(self, mongodb_handler):
        if len(self._mongodb_handlers) < self._size:
            self._mongodb_handlers.append(mongodb_handler)


class MongodbHandler:

    '''

    '''
    pass
    def __init__(self, database_url: str = None,
                 database_name: str = None):
        '''
        :param str database_url: Url for the mongodb database
        :param str database_name: Name of the database the database handler should handle
        '''
        if database_url is None:

            from libraries.configuration import default as cfg

            database_url = "mongodb://{0}:{1}@{2}:{3}"\
                           .format(cfg["MONGO"]["MONGO_USER"],
                                   cfg["MONGO"]["MONGO_PASSWORD"],
                                   cfg["MONGO"]["MONGO_HOST"],
                                   cfg["MONGO"]["MONGO_PORT"])

            if database_name is None:

                database_name = cfg["MONGO"]["MONGO_DATABASE_NAME"]

        assert(isinstance(database_url, str)),\
            "Parameter 'database_url' must be a string type"
        assert(isinstance(database_name, str)),\
            "Parameter 'database_name' must be a string type"

        self._log = Log("Mongodb Handler")

        # Connect to the MongoDB
        self._client = MongoClient(database_url)
        # Connect to the oebb_db database, or create it if it doesnt exist.
        self._database = self._client[database_name]

        self._database_name = database_name

    def __del__(self):
        try:
            self._client.close()
        except Exception as e:
            self._log.log_and_raise_error(('An error occured when trying to dispose the SQL engine. Error: {}').format(e))


    def set_database(self, database_name: str):
        '''
        :param str database_name: Name of the database.
        '''
        assert(isinstance(database_name, str)),\
            "Parameter 'database_name' must be a string type"

        if database_name not in self._client.list_database_names():
            self._log.info(('Database: {} didnt exist, it will be created for you once a collection is created in it').format(database_name))
        self._database = self._client[database_name]

    def drop_database(self):
        '''
        '''
        try:
            self._client.drop_database(self._database_name)
        except Exception as error:
            self._log.log_and_raise_error(('Couldnt drop the database. Error: {}').format(error))


    def drop_collection(self, collection_name: str):
        '''
        '''
        try:
            return_message = self._database.drop_collection(collection_name)
            if 'errmsg' in return_message:
                self._log.warning(('Couldnt drop the collection {}. Error: {}').format(collection_name, return_message['errmsg']))
        except Exception as error:
            self._log.log_and_raise_error(('Couldnt drop the collection {}. Error: {}').format(collection_name, error))

    def create_index(self, collection_name: str, key: (str, int, list), direction: (str, int)='text'):
        '''
        :param str collection_name: name on the collection for which the schema will be set.
        :param str key: Which value should be used as the index.
        :param str direction: see https://api.mongodb.com/python/current/api/pymongo/collection.html for reference.
        '''

        allowed_directions = [1, -1, '2d', 'geoHaystack', '2dsphere', 'hashed', 'text']

        assert(isinstance(collection_name, str)),\
            "Parameter 'collection_name' must be a string type"
        assert(isinstance(key, (str, int, list))),\
            "Parameter 'key' must be a string, integer or list type"
        assert(direction in allowed_directions),\
            "Parameter 'key' must be one of these values: 1, -1, '2d', 'geoHaystack', '2dsphere', 'hashed', 'text' "
        assert(isinstance(direction, str)),\
            "Parameter 'direction' must be a string type"
        if type(key) == list:

            key_list=[]
            for item in key:
                key_list.append((item,direction))

            self._database[collection_name].create_index(key_list,name='_'.join(key))
        else:
            self._database[collection_name].create_index([(key, direction)], name=key)


    def set_collection_schema(self, collection_name: str, schema_path: str,
                              validation_level: str = 'moderate',validation_action: str = 'error'):
        '''
        :param str collection_name: name on the collection for which the schema will be set.
        :param str schema_path: path to the schema file.
        :param str validation_level: level of validation done by the mongodb.
        :param str validation_action: what will happen upon validation error, warning or error message.
        '''
        assert(isinstance(collection_name, str)),\
            "Parameter 'collection_name' must be a string type"
        assert(isinstance(schema_path, str)),\
            "Parameter 'schema_path' must be a string type"
        assert(isinstance(validation_level, str)),\
            "Parameter 'validation_level' must be a string type"
        assert(isinstance(validation_action, str)),\
            "Parameter 'validation_action' must be a string type"

        parse_obj = ParseJsonSchema(schema_paths=schema_path)

        command = {
                    'collMod': collection_name,
                    'validator': {
                        '$jsonSchema': parse_obj.load_and_parse_schema_for_mongodb(schema_path)
                    },
                    'validationLevel': validation_level,
                    'validationAction': validation_action
                    }

        try:
            self._database.command(command)

        except Exception as error:
            self._log.log_and_raise_error(('An error occured when trying to set a schema for the collection: {}. \nError: {}').format(collection_name, error))

    def create_collection(self, collection_name):
        '''
        :param str collection_name: name of the collection to be created.
        '''

        assert(isinstance(collection_name, str)),\
            "Parameter 'collection_name' must be a string type"

        if collection_name not in self._database.list_collection_names():
            try:
                self._log.info(("Collection '{}' has been created").format(collection_name))
                self._database.create_collection(collection_name)

            except Exception as error:
                self._log.log_and_raise_error(('An error occured while creating the new collection: {}. \nError: {}').format(collection_name, error))
        else:
            self._log.info(("Collection '{}' already exists").format(collection_name))
            self._database[collection_name]

    def insert_data_into_collection(self, data: (dict, list, np.ndarray, pd.DataFrame, pd.Series),
                                    collection_name: str,
                                    ordered: bool = False):
        '''
        :param dict data: dictionary containing the data to be inserted in the collection
        :param pymongo.database.Collection collection: The collection the data will be added to.
        '''

        allowed_types = (dict, list, np.ndarray, pd.DataFrame, pd.Series)

        assert(isinstance(data, allowed_types)),\
            "Parameter 'data' is of invalid type"

        if isinstance(data, np.ndarray):
            data = pd.DataFrame(data)

        if isinstance(data, pd.DataFrame):

            data = simplejson.loads(data.to_json(orient="records",
                                                 date_format="iso"))

        elif isinstance(data, pd.Series):

            data = simplejson.loads(data.to_json(date_format="iso"))

        try:
            if (len(data) == 1) or (isinstance(data, dict)):

                if isinstance(data, pd.DataFrame) and (len(data) == 1):
                    insert_data = data.iloc[0]
                elif type(data) is list:
                    insert_data = data[0]
                else:
                    insert_data = data
                self._database[collection_name].insert_one(insert_data)
            else:
                self._database[collection_name].insert_many(data, ordered=ordered)

        except Exception as error:
            if len(data) > 1:

                self._log.warning(('An error occured inserting {} documents into database: {} and collection: {}.').format(len(data), self._database_name, collection_name))
                self._log.warning('This might be because one or more documents are invalid.') 
                self._log.warning('We will try to insert the documents one-by-one and report which are invalid.')
                self._log.warning(('Error: {}').format(error))
                
                for row in data:

                    try:
                        self._database[collection_name].insert_one(row)
                    except Exception as error:
                        pprint(row)
                        self._log.warning(error)
            else:
                self._log.log_and_raise_error(('An error occured when trying to insert data into {}, {}. \nError: {}').format(self._database_name, collection_name, error))

        self._log.info(('Data has been inserted into the {} collection').format(collection_name))

    def create_collection_and_set_schema(self, collection_name: str, schema_path: str):
        '''
        :param str collection_name: name of the collection to be created.
        :param str schema_path: path to the schema file.
        '''
        assert(isinstance(collection_name, str)),\
            "Parameter 'collection_name' must be a string type"
        assert(isinstance(schema_path, str)),\
            "Parameter 'schema_path' must be a string type"

        self.create_collection(collection_name)
        self.set_collection_schema(collection_name=collection_name, schema_path=schema_path)

    def query_data_and_generate_dataframe(self, collection_name: str, attribute: str = None,
                                          attribute_value: str = None, comparison_operator: str = '$eq',
                                          index = None, return_as_dataframe: bool = True, return_id: bool = False,
                                          find_query:dict = None, return_values: dict = None):
        '''

        '''
        if return_values is None:
            return_values = {'_id': return_id}

        try:
            if attribute == None or attribute_value == None:
                if find_query is None:
                    query = {}
                else:
                    query = find_query

                data = self._database[collection_name].find(query,return_values)
                
            else:
                query = {attribute: {comparison_operator: attribute_value}}
                data = self._database[collection_name].find(query, return_values)

        except Exception as error:
            self._log.log_and_raise_error(('An error occured trying to query data from {}, with query {}: {}:{}. \nError:{}').format(collection_name, attribute, comparison_operator, attribute_value, error))
            return None

        if data.collection.count_documents(query) != 0:
            if return_as_dataframe:
                return self.convert_mongo_data_into_dataframe(data, index, collection_name)
            else:
                return data

    def aggregate_data_and_generate_dataframe(self, collection_name: str, aggregation_pipeline: list, index: str = None):

        try:
            data = self._database[collection_name].aggregate(pipeline=aggregation_pipeline, allowDiskUse=True)
        except Exception as error:
            self._log.log_and_raise_error(('A problem occured when aggregating the collection {} with the pipeline {}. \nError: {}').format(collection_name, aggregation_pipeline, error))
            return None

        return self.convert_mongo_data_into_dataframe(data, index, collection_name)

    def convert_mongo_data_into_dataframe(self, data, index: str = None, collection_name: str = None, chunksize: int = 500) -> pd.DataFrame():

        start_time = time.time()
        '''
        self._log.info('Converting returned mongo data into a DataFrame')
        
        data = list(data)
        try:
            if len(data)> 0:
                if collection_name:
                    self._log.info(('{} rows were fetched from the {} collection').format(len(data), collection_name))
                else:
                    self._log.info(('{} rows were fetched from the database').format(len(data)))
                df = pd.DataFrame(data)
                if index is not None:
                    df.set_index(index, inplace=True)

                self._log.info(('DataFrame conversion is done, took {} seconds').format(time.time()-start_time))
                return df
            else:
                self._log.warning(('No data for the query was found').format())
        except Exception as error:
            self._log.log_and_raise_error(('An error occured trying to convert mongo data into pd.Dataframe. \nError: {} ').format(error))
        '''
    
        frames = []
        records = []
        for iteration, value in enumerate(data):

            records.append(value)
            if iteration + 1 % chunksize == 0:
                frames.append(pd.DataFrame(records))
                records = []

        if records:
            frames.append(pd.DataFrame(records))

        return_df = pd.concat(frames, axis=0, sort=False)

        if index is not None:
            return_df.set_index(index, inplace=True)

        self._log.info(('{} Rows were fetched from {}. DataFrame conversion is done, took {} seconds').format(len(return_df.index), collection_name if collection_name is not None else 'the database', time.time()-start_time))
        
        return return_df

 
        

    #def update_data_in_collection(self, query_label: str, query_value: str, update_label:str, update_value: str, collection_name:str):
    #    self._database[collection_name].update_one({query_label:query_value}, {"$set": {update_label: update_value}})


    def push_data_into_collection(self, data: (dict, list, np.ndarray, pd.DataFrame, pd.Series),
                                                                        collection_name: str,
                                                                        update_label: str,
                                                                        query_label: str,
                                                                        query_value: str):
        '''
            Adds data to an exising array within the collection.

            :param data: data to add
            :param str collection_name: collection to add data to
            :param str update_label: label of the attribute where data is to be added
            :param str query_label: label for the query
            :param str query_value: value for the query
        '''


        self._database[collection_name].update_one({query_label:query_value}, {"$push": {update_label: data}})
        self._log.info(('A document has been pushed into the {} array in the {} collection').format(query_value, collection_name))

    def document_exists(self, collection_name: str, query_label: str, query_value:str):
        '''
            Checking whether the document exists or not.

            :param str collection_name: collection to add data to
            :param str query_label: label for the query
            :param str query_value: value for the query
        '''
        return self._database[collection_name].find({query_label:query_value}).count() > 0

    def query_data_between_dates_and_generate_dataframe(self, collection_name: str, date_label: str, from_date_value: str, to_date_value: str, index: str = None, return_id: bool = False, return_as_dataframe: bool = True):
        '''
            Queries data between two dates.

            :param str collection_name: collection to add data to
            :param str date_label: label of the attribute where the date is stored
            :param str from_date_value: date which
            :param str to_date_value: value for the query
            :param str index:
            :param bool return_as_dataframe:
        '''
        assert(isinstance(collection_name, str)),\
            "Parameter 'collection_name' must be a string type"
        try:
            query = {date_label: {'$gt': from_date_value, '$lt': to_date_value}}
            data = self._database[collection_name].find(query, {'_id': return_id})

        except Exception as error:
            self._log.log_and_raise_error(('An error occured trying to query data from {}, with query {}. \nError:{}').format(collection_name, query, error))

        if data.collection.count_documents(query) != 0:
            if return_as_dataframe:
                return self.convert_mongo_data_into_dataframe(data, index, collection_name)
            else:
                return data

    def query_oldest_or_newest_date_in_collection(self, collection_name: str, date_label: str, oldest: bool = False):

        date = None
        direction = pymongo.ASCENDING if oldest else pymongo.DESCENDING
        try:

            data = list(self._database[collection_name].find().sort(date_label, direction).limit(1))
            if data:
                date = self.convert_mongo_data_into_dataframe(data, collection_name=collection_name)[date_label].values[0]
            else:
                self._log.warning('No date was found for this query.')

        except Exception as error:
            self._log.log_and_raise_error(('An error occured trying to query data from {}, finding the oldest: {}, value for: {}. \nError:{}').format(collection_name, oldest, date_label, error))

        return date

    def query_with_sorting_and_limit(self, collection_name: str, sort_label: str, limit:int, attribute: str = None,
                                          attribute_value: str = None, comparison_operator: str = '$eq', ascending=True,
                                          index = None, return_as_dataframe: bool = True, return_id: bool = False):

        direction = pymongo.ASCENDING if ascending else pymongo.DESCENDING
        try:

            if attribute == None or attribute_value == None:
                query = {}
                data = self._database[collection_name].find(query,{'_id': return_id}).sort(sort_label, direction).limit(limit)
            else:
                query = {attribute: {comparison_operator: attribute_value}}
                data = self._database[collection_name].find(query, {'_id': return_id}).sort(sort_label, direction).limit(limit)

        except Exception as error:
            self._log.log_and_raise_error(('An error occured trying to query data from {}, \nError:{}').format(collection_name, error))

        if data.collection.count_documents(query) != 0:
            if return_as_dataframe:
                return self.convert_mongo_data_into_dataframe(data, index, collection_name)
            else:
                return data
        else:
            self._log.warning('No data was found for the query')
            return None

    def update_data_in_collection(self, update_label:str, update_value: str, collection_name:str, query_label: str = None, query_value: str = None, create_if_not_exist: bool = True, find_query: dict = None, update_query:dict = None, update_many: bool = False):

        if isinstance(update_value, pd.DataFrame):
            update_value = simplejson.loads(update_value.to_json(orient="records",
                                                 date_format="iso"))

        if update_query is None:
            update_query = {"$set": {update_label: update_value}}

        if find_query is None:
            if query_label and query_value:
                find_query = {query_label:query_value}
                
                                             
        try:
            if update_many:
                if find_query is not None:
                    self._database[collection_name].update_many(find_query, update_query, upsert=create_if_not_exist)

                else:
                    self._database[collection_name].update_many({}, update_query, upsert=create_if_not_exist)

            else:
                if find_query is not None:
                    self._database[collection_name].update_one(find_query, update_query, upsert=create_if_not_exist)

                else:
                    self._database[collection_name].update_one({}, update_query, upsert=create_if_not_exist)

            self._log.info(('Data for label: {} has been updated').format(update_label))

        except Exception as error:
            self._log.log_and_raise_error(('There was a problem updating data for label: {}, Error: {}').format(update_label, error))



if __name__ == "__main__":

    log = Log("Test MongodbHandler:")

    log.info('Script started')

    database_url = "mongodb://{0}:{1}@{2}:{3}"\
                           .format('root',
                                   'oebb',
                                   'localhost',
                                   27017)
    database_name = 'test_database'

    db_handler = MongodbHandler(database_name=database_name, database_url=database_url)

    # Create a colleciton for the wheelsets and give it its schema.
    for schema_path in [
            os.path.join(".", "mongo_schema", "schema_wheelsets.json"),
            os.path.join(".", "mongo_schema", "schema_process_instances.json"),
            os.path.join(".", "mongo_schema", "schema_componets.json")]:

        if os.path.isfile(schema_path):

            collection_name = os.path.basename(schema_path).lstrip("_schema").split(".")[0]

            db_handler.create_collection_and_set_schema(collection_name, schema_path)
        else:
            log.log_and_raise_warning(('No file exists at path: {}').format(schema_path))

    log.info(("Existing databases: {}, Collection in OEBB database {}")\
             .format(db_handler._client.list_database_names(), db_handler._database.list_collection_names()))