Issue
I recently encountered a challenge in Azure Data Lake Analytics when I attempted to read in a Large UTF-8 JSON Array file and switched to HDInsight PySpark (v2.x, not 3) to process the file. The file is ~110G and has ~150m JSON Objects.
HDInsight PySpark does not appear to support Array of JSON file format for input, so I'm stuck. Also, I have "many" such files with different schemas in each containing hundred of columns each, so creating the schemas for those is not an option at this point.
Question
How do I use out-of-the-box functionality in PySpark 2 on HDInsight to enable these files to be read as JSON?
Thanks,
J
Things I tried
I used the approach at the bottom of this page:
from Databricks that supplied the below code snippet:
import json
df = sc.wholeTextFiles('/tmp/*.json').flatMap(lambda x: json.loads(x[1])).toDF()
display(df)
I tried the above, not understanding how "wholeTextFiles" works, and of course ran into OutOfMemory errors that killed my executors quickly.
I attempted loading to an RDD and other open methods, but PySpark appears to support only the JSONLines JSON file format, and I have the Array of JSON Objects due to ADLA's requirement for that file format.
I tried reading in as a text file, stripping Array characters, splitting on the JSON object boundaries and converting to JSON like the above, but that kept giving errors about being unable to convert unicode and/or str (ings).
I found a way through the above, and converted to a dataframe containing one column with Rows of strings that were the JSON Objects. However, I did not find a way to output only the JSON Strings from the data frame rows to an output file by themselves. The always came out as
{'dfColumnName':'{...json_string_as_value}'}
I also tried a map function that accepted the above rows, parsed as JSON, extracted the values (JSON I wanted), then parsed the values as JSON. This appeared to work, but when I would try to save, the RDD was type PipelineRDD and had no saveAsTextFile() method. I then tried the toJSON method, but kept getting errors about "found no valid JSON Object", which I did not understand admittedly, and of course other conversion errors.
I finally found a way forward. I learned that I could read json directly from an RDD, including a PipelineRDD. I found a way to remove the unicode byte order header, wrapping array square brackets, split the JSON Objects based on a fortunate delimiter, and have a distributed dataset for more efficient processing. The output dataframe now had columns named after the JSON elements, inferred the schema, and dynamically adapts for other file formats.
Here is the code - hope it helps!:
#...Spark considers arrays of Json objects to be an invalid format
# and unicode files are prefixed with a byteorder marker
#
thanksMoiraRDD = sc.textFile( '/a/valid/file/path', partitions ).map(
lambda x: x.encode('utf-8','ignore').strip(u",\r\n[]\ufeff")
)
df = sqlContext.read.json(thanksMoiraRDD)
Related
I basically have a procedure where I make multiple calls to an API and using a token within the JSON return pass that pack to a function top call the API again to get a "paginated" file.
In total I have to call and download 88 JSON files that total 758mb. The JSON files are all formatted the same way and have the same "schema" or at least should do. I have tried reading each JSON file after it has been downloaded into a data frame, and then attempted to union that dataframe to a master dataframe so essentially I'll have one big data frame with all 88 JSON files read into.
However the problem I encounter is roughly on file 66 the system (Python/Databricks/Spark) decides to change the file type of a field. It is always a string and then I'm guessing when a value actually appears in that field it changes to a boolean. The problem is then that the unionbyName fails because of different datatypes.
What is the best way for me to resolve this? I thought about reading using "extend" to merge all the JSON files into one big file however a 758mb JSON file would be a huge read and undertaking.
Could the other solution be to explicitly set the schema that the JSON file is read into so that it is always the same type?
If you know the attributes of those files, you can define the schema before reading them and create an empty df with that schema so you can to a unionByName with the allowMissingColumns=True:
something like:
from pyspark.sql.types import *
my_schema = StructType([
StructField('file_name',StringType(),True),
StructField('id',LongType(),True),
StructField('dataset_name',StringType(),True),
StructField('snapshotdate',TimestampType(),True)
])
output = sqlContext.createDataFrame(sc.emptyRDD(), my_schema)
df_json = spark.read.[...your JSON file...]
output.unionByName(df_json, allowMissingColumns=True)
I'm not sure this is what you are looking for. I hope it helps
I'm trying to understand the code for reading JSON file in Synapse Analytics. And here's the code provided by Microsoft documentation:
Query JSON files using serverless SQL pool in Azure Synapse Analytics
select top 10 *
from openrowset(
bulk 'https://pandemicdatalake.blob.core.windows.net/public/curated/covid-19/ecdc_cases/latest/ecdc_cases.jsonl',
format = 'csv',
fieldterminator ='0x0b',
fieldquote = '0x0b'
) with (doc nvarchar(max)) as rows
go
I wonder why the format = 'csv'. Is it trying to convert JSON to CSV to flatten the file?
Why they didn't just read the file as a SINGLE_CLOB I don't know
When you use SINGLE_CLOB then the entire file is important as one value and the content of the file in the doc is not well formatted as a single JSON. Using SINGLE_CLOB will make us do more work after using the openrowset, before we can use the content as JSON (since it is not valid JSON we will need to parse the value). It can be done but will require more work probably.
The format of the file is multiple JSON's like strings, each in separate line. "line-delimited JSON", as the document call it.
By the way, If you will check the history of the document at GitHub, then you will find that originally this was not the case. As much as I remember, originally the file included a single JSON document with an array of objects (was wrapped with [] after loaded). Someone named "Ronen Ariely" in fact found this issue in the document, which is why you can see my name in the list if the Authors of the document :-)
I wonder why the format = 'csv'. Is it trying to convert json to csv to flatten the hierarchy?
(1) JSON is not a data type in SQL Server. There is no data type name JSON. What we have in SQL Server are tools like functions which work on text and provide support for strings which are JSON's like format. Therefore, we do not CONVERT to JSON or from JSON.
(2) The format parameter has nothing to do with JSON. It specifies that the content of the file is a comma separated values file. You can (and should) use it whenever your file is well formatted as comma separated values file (also commonly known as csv file).
In this specific sample in the document, the values in the csv file are strings, which each one of them has a valid JSON format. Only after you read the file using the openrowset, we start to parse the content of the text as JSON.
Notice that only after the title "Parse JSON documents" in the document, the document starts to speak about parsing the text as JSON.
Snowflake supports multiple file types via creation FILE_FORMAT (avro, json, csv etc).
Now I have tested SELECTing from snowflake stage (s3) both:
*.avro files (generated from nifi processor batching 10k source oracle table).
*.json files (json per line).
And when Select $1 from #myStg, snowflake expands as many rows as records on avro or json files (cool), but.. the $1 variant is both json format and now i wonder if whatever snowflake file_format we use do records always arrive as json on the variant $1 ?
I haven't tested csv or others snowflake file_formats.
Or i wonder if i get json from the avros (from oracle table) because maybe NiFi processor creates avro files (with internally uses json format).
Maybe im making some confusion here.. i know avro files contain both:
avro schema - language similar to json key/value.
compressed data (binary).
Thanks,
Emanuel O.
I tried with CSV, When Its came to CSV its parsing each records in the file like below
So when its came to JSON it will treat one complete JSON as one records so its displaying in JSON format.
I have a sequence file containing multiple json records. I want to send every json record to a function . How can I extract one json record at a time?
Unfortunately there is no standard way to do this.
Unlike YAML which has a well-defined way to allow one file contain multiple YAML "documents", JSON does not have such standards.
One way to solve your problem is to invent your own "object separator". For example, you can use newline characters to separate adjacent JSON objects. You can tell your JSON encoder not to output any newline characters (by forcing escaping it into \ and n). As long as your JSON decoder is sure that it will not see any newline character unless it separates two JSON objects, it can read the stream one line at a time and decode each line.
It has also been suggested that you can use JSON arrays to store multiple JSON objects, but it will no longer be a "stream".
You can read content of your sequence files to RDD[String] and convert it to Spark Dataframe.
val seqFileContent = sc
.sequenceFile[LongWritable, BytesWritable](inputFilename)
.map(x => new String(x._2.getBytes))
val dataframeFromJson = sqlContext.read.json(seqFileContent)
I'm trying to write output from a scalding flow in json form, and reading it in Spark. This is working fine, except if the json contains strings with new lines. The output is one json object per line, and newlines in a value on the json is causing one bit of json to be fragmented across two lines. As such, when I read lines into Spark, I can't deserialize some of them. Is there a standard way to deal with this?