Problem description: I am trying to update documents in elastic search. I have data in a dataframe. Dataframe has esIndex, id and body attributes. I need to use the value in index attribute to update the document in the right index. The following code below does not work. What is possible fix?
Command 1
val esUrl = "test.elasticsearch.com"
Command 2
import spark.implicits._
val df = Seq(
("test_datbricks001","1221866122238136328", "TEST DATA 001"),
("test_datbricks001","1221866122238136329", "TEST DATA 002"),
("test_datbrick","1221866122238136329", "TEST DATA 002")
).toDF("esIndex", "id", "body")
Command 3
display(df)
Command 4
import org.apache.spark.sql.functions.col
val retval = df.toDF.write
.format("org.elasticsearch.spark.sql")
.option("es.nodes.wan.only","true")
.option("es.mapping.id","id")
.option("es.mapping.exclude", "id, esIndex")
.option("es.port","80")
.option("es.nodes", esUrl)
.option("es.write.operation", "update")
.option("es.index.auto.create", "no")
.mode("Append")
.save("{esIndex}") // <<== This index is not taking value from "index" column of df
I am getting the following error EsHadoopIllegalArgumentException: Target index [{esIndex}] does not exist and auto-creation is disabled [setting 'es.index.auto.create' is 'false']
Question: How do I get code in Command 4 to use the value in esIndex column of df
Related
Hi i'm having an issue with the transfer of data from one database to another. I created a list using field in a table on a msql db, used that list to query and oracle db table (using the initial list in the where statement to filter results) I then load the query results back into the msql db.
The program runs for the first few iterations but then errors out, with the following error (
Traceback (most recent call last):
File "C:/Users/1/PycharmProjects/DataExtracts/BuyerGroup.py", line 67, in
insertIntoMSDatabase(idString)
File "C:/Users/1/PycharmProjects/DataExtracts/BuyerGroup.py", line 48, in insertIntoMSDatabase
mycursor.executemany(sql, val)
pyodbc.ProgrammingError: The second parameter to executemany must not be empty.)
I can't seem to find and guidance online to troubleshoot this error message. I feel it may be a simple solution but I just can't get there...
# import libraries
import cx_Oracle
import pyodbc
import logging
import time
import re
import math
import numpy as np
logging.basicConfig(level=logging.DEBUG)
conn = pyodbc.connect('''Driver={SQL Server Native Client 11.0};
Server='servername';
Database='dbname';
Trusted_connection=yes;''')
b = conn.cursor()
dsn_tns = cx_Oracle.makedsn('Hostname', 'port', service_name='name')
conn1 = cx_Oracle.connect(user=r'uid', password='pwd', dsn=dsn_tns)
c = conn1.cursor()
beginTime = time.time()
bind = (b.execute('''select distinct field1
from [server].[db].[dbo].[table]'''))
print('MSQL table(s) queried, List Generated')
# formats ids for sql string
def surroundWithQuotes(id):
return "'" + re.sub(",|\s$", "", str(id)) + "'"
def insertIntoMSDatabase(idString):
osql = '''SELECT distinct field1, field2
FROM Database.Table
WHERE field2 is not null and field3 IN ({})'''.format(idString)
c.execute(osql)
claimsdata = c.fetchall()
print('Oracle table(s) queried, Data Pulled')
mycursor = conn.cursor()
sql = '''INSERT INTO [dbo].[tablename]
(
[fields1]
,[field2]
)
VALUES (?,?)'''
val = claimsdata
mycursor.executemany(sql, val)
conn.commit()
ids = []
formattedIdStrings = []
# adds all the ids found in bind to an iterable array
for row in bind:
ids.append(row[0])
# splits the ids[] array into multiple arrays < 1000 in length
batchedIds = np.array_split(ids, math.ceil(len(ids) / 1000))
# formats the value inside each batchedId to be a string
for batchedId in batchedIds:
formattedIdStrings.append(",".join(map(surroundWithQuotes, batchedId)))
# runs insert into MS database for each batch of IDs
for idString in formattedIdStrings:
insertIntoMSDatabase(idString)
print("MSQL table loaded, Data inserted into destination")
endTime = time.time()
print("Program Time Elapsed: ",endTime-beginTime)
conn.close()
conn1.close()
mycursor.executemany(sql, val)
pyodbc.ProgrammingError: The second parameter to executemany must not be empty.
Before calling .executemany() you need to verify that val is not an empty list (as would be the case if .fetchall() is called on a SELECT statement that returns no rows) , e.g.,
if val:
mycursor.executemany(sql, val)
My Elasticsearch index has more than 1000 fields due to my Sql schema and I get below exception:
{'type': 'illegal_argument_exception', 'reason': 'Limit of total
fields [1000] in index }
And my bulk insert looks like this:
with open('audit1.txt') as file:
for line in file:
columns = line.split(r'||')
dict['TimeStamp']=columns[0].strip('\'')
dict['BusinessTimeStamp']=columns[1].strip('\'')
dict['RuntimeMicroflowID']=columns[2].strip('\'')
dict['MicroflowID']=columns[3].strip('\'')
dict['UserId']=columns[4].strip('\'')
dict['ClientId']=columns[5].strip('\'')
dict['Userlocation']=columns[6].strip('\'')
dict['Transactionid']=columns[7].strip('\'')
dict['Catagorie']=columns[8].strip('\'')
dict['EventType']=columns[9].strip('\'')
dict['Operation']=columns[10].strip('\'')
dict['PrimaryData']=columns[11].strip('\'')
dict['SecondayData']=columns[12].strip('\'')
i=13
while i < len(columns):
tempdict['BFOLDVALUE'] = columns[i+1].strip('\'')
tempdict['BFNEWVALUE'] = columns[i+2].strip('\'')
if columns[i].strip('\'') is not None:
dict[columns[i].strip('\'')] = tempdict.copy()
i+=3
tempdict.clear()
#print(json.dumps(dict,indent = 4))
batch.append(dict)
if counter==BATCHSIZE:
try:
helpers.bulk(es, batch, index='audit-index', doc_type='audit')
insertedrecords+=counter
counter = 0
batch.clear()
print(insertedrecords," - Records Has Been inserted ")
except BulkIndexError:
print("Error Occured -- continuing")
print(json.dumps(dict,indent = 4))
print(BulkIndexError)
batch.clear()
break
counter+=1
dict.clear()
So, I am assuming I am trying to index this wrongly... is there a better way of indexing this kind of formats in elasticsearch? Note than I am using ELK version 7.5.
Here is the sample file I am parsing to elasticsearch:
2018.07.17/15:41:53.735||2018.07.17/15:41:53.735||'0164a8424fbbp84h%2139165'||'BT_TTB_CashDep_PRC'||'eskedarz'||'UXP'||'00001039'||'0164a842e519pJpA'||'Persistence'||''||'CREATE'||'DailyTxns'||'0164a842e4eapJnu'||'CurrentThread'||'WebContainer : 15'||''||'ParentThread'||'system'||''||'TCPWorkerThreadID'||'WebContainer : 15'||''||'f_POSTINGDT'||'2018-07-17'||''||'versionNum'||'0'||''||'f_TXNAMTDR'||'0'||''||'f_ACCOUNTID'||'013XXXXXXXXX0'||''||'f_VALUEDTTM'||'2018-07-17 15:41:53.0'||''||'f_POSTINGDTTM'||'2018-07-17 15:41:53.692'||''||'f_TXNCLBAL'||'25551.610000'||''||'f_TXNREF'||'0000103917071815410685326'||''||'f_PIEVENTTYPE'||'N'||''||'f_TXNAMT'||'5000.00'||''||'f_TRANSACTIONID'||'0164a842e4e9pJng'||''||'f_TYPE'||'N'||''||'f_USERID'||'xxxarz'||''||'f_SRNO'||'1'||''||'f_TXNBASEEQ'||'5000.00'||''||'f_TXNSRCBRANCH'||'0000X039'||''||'f_TXNCODE'||'T08'||''||'f_CHANNELID'||'BranchTeller'||''||'f_TXNAMTCR'||'5000.00'||''||'f_TXNNARRATION'||'SELF '||''||'f_ISACCRUALPENDING'||'false'||''||'f_TXNDTTM'||'2018-07-17 15:41:53.689'||''
if you carefully look at this part of the error message it would be clear.
Limit of total fields [1000] in index
1000 is the default limit of total fields in the Elasticsearch index as shown in their source code.
public static final Setting<Long> INDEX_MAPPING_TOTAL_FIELDS_LIMIT_SETTING =
Setting.longSetting("index.mapping.total_fields.limit", 1000L, 0, Property.Dynamic, Property.IndexScope);
Please note this is a dynamic setting, hence can be changed on a given index, by updating index setting
PUT test_index/_settings
{
"index.mapping.total_fields.limit": 1500. --> changed it to what is suitable for your index.
}
More info on this issue can be found here and here.
better way to handle such exploding index is to normalize as RDBMS that means store some of the key : value combinations in a nested structure
example
{"keyA":"ValueA","keyB":"ValueB","keyC":"ValueC"...} - record to
{"keyA":"ValueA","Keyvalue":{"keyB":"ValueB"
"keyC":"ValueC"}} - record
so searching would look like Keyvalue.Value == KeyB and KeyValue.Value = ValueB
Spark Version: '2.0.0.2.5.0.0-1245'
So, my original question changed a bit but it's still the same issue.
What I want to do is load a huge amount of JSON files and transform those to a DataFrame - also probably save them as CSV or parquet file for further processing. Each JSON file represents one row in the final DataFrame.
import os
import glob
HDFS_MOUNT = # ...
DATA_SET_BASE = # ...
schema = StructType([
StructField("documentId", StringType(), True),
StructField("group", StringType(), True),
StructField("text", StringType(), True)
])
# Get the file paths
file_paths = glob.glob(os.path.join(HDFS_MOUNT, DATA_SET_BASE, '**/*.json'))
file_paths = [f.replace(HDFS_MOUNT + '/', '') for f in file_paths]
print('Found {:d} files'.format(len(file_paths))) # 676 files
sql = SQLContext(sc)
df = sql.read.json(file_paths, schema=schema)
print('Loaded {:d} rows'.format(df.count())) # 9660 rows (what !?)
Besides the fact that there are 9660 rows instead of 676 (number of available files) I also have the problem that the content seems to be None:
df.head(2)[0].asDict()
gives
{
'documentId': None,
'group': None,
'text': None,
}
Example Data
This is just fake data of course but it resembles the actual data.
Note: Some fields may be missing e.g. text must not always be present.
a.json
{
"documentId" : "001",
"group" : "A",
"category" : "indexed_document",
"linkIDs": ["adiojer", "asdi555", "1337"]
}
b.json
{
"documentId" : "002",
"group" : "B",
"category" : "indexed_document",
"linkIDs": ["linkId", "1000"],
"text": "This is the text of this document"
}
assuming that all your files has the same structure and are in the same directory:
df = sql_cntx.read.json('/hdfs/path/to/folder/*.json')
There might be a problem if any of the columns has Null values for all rows. Then spark will not be able to determine schema, so you have an option to tell spark which schema to use:
from pyspark import SparkContext, SQLContext
from pyspark.sql.types import StructType, StructField, StringType, LongType
sc = SparkContext(appName="My app")
sql_cntx = SQLContext(sc)
schema = StructType([
StructField("field1", StringType(), True),
StructField("field2", LongType(), True)
])
df = sql_cntx.read.json('/hdfs/path/to/folder/*.json', schema=schema)
UPD:
in case if file has multirows formatted json you can try this code:
sc = SparkContext(appName='Test')
sql_context = SQLContext(sc)
rdd = sc.wholeTextFiles('/tmp/test/*.json').values()
df = sql_context.read.json(rdd, schema=schema)
df.show()
I needed a stable index sorting for DataFrames, when I had this problem:
In cases where a DataFrame becomes a Series (when only a single column matches the selection), the kind argument returns an error. See example:
import pandas as pd
df_a = pd.Series(range(10))
df_b = pd.Series(range(100, 110))
df = pd.concat([df_a, df_b])
df.sort_index(kind='mergesort')
with the following error:
----> 6 df.sort_index(kind='mergesort')
TypeError: sort_index() got an unexpected keyword argument 'kind'
If DataFrames (more then one column is selected), mergesort works ok.
EDIT:
When selecting a single column from a DataFrame for example:
import pandas as pd
import numpy as np
df_a = pd.DataFrame(np.array(range(25)).reshape(5,5))
df_b = pd.DataFrame(np.array(range(100, 125)).reshape(5,5))
df = pd.concat([df_a, df_b])
the following returns an error:
df[0].sort_index(kind='mergesort')
...since the selection is casted to a pandas Series, and as pointed out the pandas.Series.sort_index documentation contains a bug.
However,
df[[0]].sort_index(kind='mergesort')
works alright, since its type continues to be a DataFrame.
pandas.Series.sort_index() has no kind parameter.
here is the definition of this function for Pandas 0.18.1 (file: ./pandas/core/series.py):
# line 1729
#Appender(generic._shared_docs['sort_index'] % _shared_doc_kwargs)
def sort_index(self, axis=0, level=None, ascending=True, inplace=False,
sort_remaining=True):
axis = self._get_axis_number(axis)
index = self.index
if level is not None:
new_index, indexer = index.sortlevel(level, ascending=ascending,
sort_remaining=sort_remaining)
elif isinstance(index, MultiIndex):
from pandas.core.groupby import _lexsort_indexer
indexer = _lexsort_indexer(index.labels, orders=ascending)
indexer = com._ensure_platform_int(indexer)
new_index = index.take(indexer)
else:
new_index, indexer = index.sort_values(return_indexer=True,
ascending=ascending)
new_values = self._values.take(indexer)
result = self._constructor(new_values, index=new_index)
if inplace:
self._update_inplace(result)
else:
return result.__finalize__(self)
file ./pandas/core/generic.py, line 39
_shared_doc_kwargs = dict(axes='keywords for axes', klass='NDFrame',
axes_single_arg='int or labels for object',
args_transpose='axes to permute (int or label for'
' object)')
So most probably it's a bug in the pandas documentation...
Your df is Series, it's not a data frame
I am trying to read this json file into a hive table, the top level keys i.e. 1,2.., here are not consistent.
{
"1":"{\"time\":1421169633384,\"reading1\":130.875969,\"reading2\":227.138275}",
"2":"{\"time\":1421169646476,\"reading1\":131.240628,\"reading2\":226.810211}",
"position": 0
}
I only need the time and readings 1,2 in my hive table as columns ignore position.
I can also do a combo of hive query and spark map-reduce code.
Thank you for the help.
Update , here is what I am trying
val hqlContext = new HiveContext(sc)
val rdd = sc.textFile(data_loc)
val json_rdd = hqlContext.jsonRDD(rdd)
json_rdd.registerTempTable("table123")
println(json_rdd.printSchema())
hqlContext.sql("SELECT json_val from table123 lateral view explode_map( json_map(*, 'int,string')) x as json_key, json_val ").foreach(println)
It throws the following error :
Exception in thread "main" org.apache.spark.sql.hive.HiveQl$ParseException: Failed to parse: SELECT json_val from temp_hum_table lateral view explode_map( json_map(*, 'int,string')) x as json_key, json_val
at org.apache.spark.sql.hive.HiveQl$.createPlan(HiveQl.scala:239)
at org.apache.spark.sql.hive.ExtendedHiveQlParser$$anonfun$hiveQl$1.apply(ExtendedHiveQlParser.scala:50)
at org.apache.spark.sql.hive.ExtendedHiveQlParser$$anonfun$hiveQl$1.apply(ExtendedHiveQlParser.scala:49)
at scala.util.parsing.combinator.Parsers$Success.map(Parsers.scala:136)
at scala.util.parsing.combinator.Parsers$Success.map(Parsers.scala:135)
at scala.util.parsing.combinator.Parsers$Parser$$anonfun$map$1.apply(Parsers.scala:242)
at scala.util.parsing.combinator.Parsers$Parser$$anonfun$map$1.apply(Parsers.scala:242)
at scala.util.parsing.combinator.Parsers$$anon$3.apply(Parsers.scala:222)
This would work, if you rename "1" and "2" (key names) to "x1" and "x2" (inside the json file or in the rdd):
val resultrdd = sqlContext.sql("SELECT x1.time, x1.reading1, x1.reading1, x2.time, x2.reading1, x2.reading2 from table123 ")
resultrdd.flatMap(row => (Array( (row(0),row(1),row(2)), (row(3),row(4),row(5)) )))
This would give you an RDD of tuples with time, reading1 and reading2. If you need a SchemaRDD, you would map it to a case class inside the flatMap transformation, like this:
case class Record(time: Long, reading1: Double, reading2: Double)
resultrdd.flatMap(row => (Array( Record(row.getLong(0),row.getDouble(1),row.getDouble(2)),
Record(row.getLong(3),row.getDouble(4),row.getDouble(5)) )))
val schrdd = sqlContext.createSchemaRDD(resultrdd)
Update:
In the case of many nested keys, you can parse the row like this:
val allrdd = sqlContext.sql("SELECT * from table123")
allrdd.flatMap(row=>{
var recs = Array[Record]();
for(col <- (0 to row.length-1)) {
row(col) match {
case r:Row => recs = recs :+ Record(r.getLong(2),r.getDouble(0),r.getDouble(1));
case _ => ;
}
};
recs
})