Load JSON data into BigQuery table - json

I'm trying to load simple JSON data into BigQuery table the following way:
$ bq load \
--apilog \
--source_format=NEWLINE_DELIMITED_JSON \
my_dataset.my_table \
./input.json ./schema.json
but get the following error message:
Upload complete.
Waiting on bqjob_xxxx_xxx ... (3s) Current status: DONE
BigQuery error in load operation: Error processing job 'my_project_id:bqjob_xxxx_xxx': CSV table encountered too many errors, giving up. Rows: 1; errors: 1.
Failure details:
- file-00000000: Error detected while parsing row starting at
position: 0. Error: Data between close double quote (") and field
separator.
It complains about some CSV error, but I'm trying to load JSON (--source_format=NEWLINE_DELIMITED_JSON)
My input.json contains this data:
{"domain":"stackoverflow.com","key":"hello","value":"world"}
My schema.json is the following:
[
{
"name": "domain",
"type": "string",
"mode": "nullable"
},
{
"name": "key",
"type": "string",
"mode": "nullable"
},
{
"name": "value",
"type": "string",
"mode": "nullable"
}
]
bq version 2.0.25:
$ gcloud version | grep ^bq
bq 2.0.25

The problem here is that the flag apilog expects a string as input. This command should work for you:
bq load \
--apilog '' \
--source_format=NEWLINE_DELIMITED_JSON \
my_dataset.my_table \
./input.json ./schema.json
Empty string sends output to stdout. If you want to save the log to a local file then you can just send a non-empty string, such as --apilog 'localfile_name'.

BQ command says:
USAGE: bq.py [--global_flags] <command> [--command_flags] [args]
As you see there are global_flags and command_flags
For the global_flags that have values you need to use the equal sign:
--flag=value
The command_flags are either boolean:
--[no]replace
Or they take arguments that must follow the flag:
--source_format NEWLINE_DELIMITED_JSON
Also do not mix global and command flags: apilog is a global flag.
I would rewrite your command into:
$ bq --apilog load \
--source_format NEWLINE_DELIMITED_JSON \
my_dataset.my_table \
./input.json ./schema.json

Related

Import JSON content from CSV file using spark

Currently, I’m working with the following architecture.
I do have a DocumentDB database that has data exported to S3 using DMS (CDC task), once this data is landed on S3 I need to load it into Databricks.
I’m already able to read the CSV content (which has a lot of JSONS), but I don't how to parse/insert it into a Databricks table.
Following my JSON payload which is exported to S3.
{
"_id": {
"$oid": "12332334"
},
"processed": false,
"col1": "0000000122",
"startedAt": {
"$date": 1635667097000
},
"endedAt": {
"$date": 1635667710000
},
"col2": "JFHFGALJF-DADAD",
"col3": 2.75,
"created_at": {
"$date": 1635726018693
},
"updated_at": {
"$date": 1635726018693
},
"__v": 0
}
To extract the data into Daframe I'm using the following spark command:
df = spark.read \
.option("header", "true") \
.option("delimiter", "|") \
.option("inferSchema", "false" ) \
.option("lineterminator", "\n" ) \
.option("encoding", "ISO-8859-1") \
.option("ESCAPE quote", '"') \
.option("escape", "\"") \
.csv("dbfs:/mnt/s3-data-2/folder_name/LOAD00000001.csv")
Thank you Alex Ott as per your Suggestion and as per this document. you can use from_json in your file to read JSON to CSV
In order to read a JSON string from a CSV file, first, we need to read a CSV file into Spark Dataframe using spark.read.csv("path") and then parse the JSON string column and convert it to columns using from_json() function. This function takes the first argument as a JSON column name and the second argument as JSON schema.

How to parse json values stored in shell variable

#!/bin/bash
DESCRIBE_VPC=$(aws ec2 describe-vpcs --region us-west-2)
The Json value retrieved from aws ec2 describe-vpcs --region us-west-2 stores in DESCRIBE_VPC which comes to the output format below.
> echo $DESCRIBE_VPC
{
"Vpcs": [
{
"VpcId": "vpc-12345678910",
"InstanceTenancy": "default",
"Tags": [
{
"Value": "arn:aws:cloudformation:us-west-2:12345678910:stack/vpc/0123456-vpcid",
"Key": "stack-id"
},
{
"Value": "vpc-type",
"Key": "Name"
},
],
"CidrBlockAssociationSet": [
{
"AssociationId": "vpc-cidr-123456",
"CidrBlock": "123.456.89.10",
"CidrBlockState": {
"State": "associated"
}
}
],
"State": "available",
"DhcpOptionsId": "dpt-01234567",
"OwnerId": "12345678910",
"CidrBlock": "123.456.789.10",
"IsDefault": false
}
]
}
[root#ip bin]# jq '.Vpcs' $DESCRIBE_VPC
jq: error: Could not open file {: No such file or directory
jq: error: Could not open file "Vpcs":: No such file or directory
parse error: Invalid numeric literal at line 1, column 57
Any suggestions here how to parse the json values stored in variable?
Actually you have to use the (json) content of a shell variable in place of a command's (jq) input. This input should be a file or a stream, but you have it in a shell variable. There are many ways to do this, this is a simple one:
echo "$DESCRIBE_VPC" | jq '.Vpcs'
or
printf "%s" "$DESCRIBE_VPC" | jq '.Vpcs'
or this (for bash shell):
jq '.Vpcs' <<< "$DESCRIBE_VPC"
Also jq can accept variables and json variables. For example you could do this:
jq -n --argjson x "$DESCRIBE_VPC" '$x.Vpcs'
But the first one is usually better.

Why is my jq failing on my JSON?

Haven't used jq before but I'm wanting to build a shell script that will get a JSON response and extract just the values. To learn I thought I would try on my blog's WP API but for some reason I'm getting an error of:
jq: error (at :322): Cannot index array with string "slug"
When researching for and testing previous questions:
jq: Cannot index array with string
jq is sed for JSON
JSON array to bash variables using jq
How to use jq in a shell pipeline?
How to extract data from a JSON file
The above reading I've tried to code:
URL="http://foobar.com"
RESPONSE=$(curl -so /dev/null -w "%{http_code}" $URL)
WPAPI="/wp-json/wp/v2"
IDENTIFIER="categories"
if (("$RESPONSE" == 200)); then
curl -s {$URL$WPAPI"/"$IDENTIFIER"/"} | jq '.' >> $IDENTIFIER.json
result=$(jq .slug $IDENTIFIER.json)
echo $result
else
echo "Not returned status 200";
fi
An additional attempt changing the jq after the curl:
curl -s {$URL$WPAPI"/"$IDENTIFIER"/"} | jq '.' | $IDENTIFIER.json
result=(jq -r '.slug' $IDENTIFIER.json)
echo $result
I can modify the uncompress with the python JSON tool:
result=(curl -s {$URL$WPAPI"/"$IDENTIFIER"/"} | python -m json.tool > $IDENTIFIER.json)
I can save the JSON to a file but when I use jq I cannot get just the slug and here are my other trys:
catCalled=$(curl -s {$URL$WPAPI"/"$IDENTIFIER"/"} | python -m json.tool | ./jq -r '.slug')
echo $catCalled
My end goal is to try to use jq in a shell script and build a slug array with jq. What am I doing wrong in my jq and can I use jq on a string without creating a file?
Return from curl after uncompress per comment request:
[
{
"id": 4,
"count": 18,
"description": "",
"link": "http://foobar.com/category/foo/",
"name": "Foo",
"slug": "foo",
"taxonomy": "category",
},
{
"id": 8,
"count": 9,
"description": "",
"link": "http://foobar.com/category/bar/",
"name": "Bar",
"slug": "bar",
"taxonomy": "category",
},
{
"id": 5,
"count": 1,
"description": "",
"link": "http://foobar.com/category/mon/",
"name": "Mon",
"slug": "mon",
"taxonomy": "category",
},
{
"id": 11,
"count": 8,
"description": "",
"link": "http://foobar.com/category/fort/",
"name": "Fort",
"slug": "fort",
"taxonomy": "category",
}
]
eventually my goal is trying to get the name of the slug's into an array like:
catArray=('foo','bar','mon', 'fort')
There are 2 issues here:
slug is not a root level element in your example json. The root level element is an array. If you want to access the slug property of each element of the array, you can do so like this:
jq '.[].slug' $IDENTIFIER.json
Your example json has trailing commas after the last property of each array element. Remove the commas after "taxonomy": "category".
If I take your sample json, remove the errant commas, save it to a plain text file called test.json and run the following command:
jq '.[].slug' test.json
I get the following output:
"foo"
"bar"
"mon"
"fort"
Preprocessing
Unfortunately, the JSON-like data shown as having been produced by curl is not strictly JSON. jq does not have a "relaxed JSON" mode, so in order to use jq, you will have to preprocess the JSON-like data, e.g. using hjson (see http://hjson.org/):
$ hjson -j input.qjson > input.json
jq
With the JSON in input.json:
$ jq -c 'map(.slug)' input.json
["foo","bar","mon","fort"]
your string is not json, notice how the last member of your objects ends with a comma,
{foo:"bar",baz:9,}
this is legal in javascript, but it's illegal in json. if you are supposed to be receiving json from that endpoint, then contact the people behind it and tell them to fix the bug (it's breaking the json specs by ending objects's last member with a comma, which is illegal in json.) - until it's fixed, i guess you can patch it with a little regex, but it's a dirty quickfix, and probably not very reliable, but running it through
perl -p -0777 -e 's/\"\,\s*}/\"}/g;' makes it legal json..

mongoexport - Leaf Level - JSON to CSV conversion - egrep not working with multiple patterns using "|" pipe or with -f option

Why egrep is not giving me all the matching entries?
This is my simple JSON blob:
[nukaNUKA#dev-machine csv]$ cat jsonfile.json
{"number": 303,"projectName": "giga","queueId":8881,"result":"SUCCESS"}
This is my pattern file (so that I don't scare the editor):
[nukaNUKA#dev-machine csv]$ cat egrep-pattern.txt
\"number\":.*\"projectName
\"projectName\":.*,\"queueId
\"queueId\":.*,\"result
\"result\":\".*$
This is egrep/grep command for individual searches, which works!:
[nukaNUKA#dev-machine csv]$ egrep -o "\"number\":.*\"projectName" jsonfile.json
"number": 303,"projectName
[nukaNUKA#dev-machine csv]$ egrep -o "\"projectName\":.*,\"queueId" jsonfile.json
"projectName": "giga","queueId
[nukaNUKA#dev-machine csv]$ egrep -o "\"queueId\":.*,\"result" jsonfile.json
"queueId":8881,"result
[nukaNUKA#dev-machine csv]$ egrep -o "\"result\":\".*$" jsonfile.json
"result":"SUCCESS"}
So, wth this didn't work? I don't wear glasses, yes.
[nukaNUKA#dev-machine csv]$ egrep -o "\"number\":.*\"projectName|\"projectName\":.*,\"queueId|\"queueId\":.*,\"result|\"result\":\".*$" jsonfile.json
"number": 303,"projectName
"queueId":8881,"result
[nukaNUKA#dev-machine csv]$ egrep -o -f egrep-pattern.txt jsonfile.json
"number": 303,"projectName
"queueId":8881,"result
[nukaNUKA#dev-machine csv]$
I have a complex nested JSON blob and because everything is unstructured, it seems like, I can't use JQ or JSONV or anything other Python script (as the data that I'm looking for is stored in arrays containing 1 dictionary entries (key=value) with same key names for what I'm looking for (ex: { "parameters": [ { "name": "jobname", "value": "shenzi" }, { "name": "pipelineVersion", "value": "1.2.3.4" }, ...so on..., ... ]) and the index for jobname and pipelineVersion or similar parameter names is not at the same index[X] location in every JSON entry I have.
Worst case, I can add conditional checks to see if the key at every index matches, jobname etc and then I get those fields what I looking for, but then, there are hundreds of such fields that I want to grab. I don't want to hard code those if possible.
I thought as my JSON entry is per line, I can simply write a cool patterns (ugly I know) but at least then I don't need to worry about the conditional code or just use BASH/sed/tr/cut power to get what I need but it seems like egrep -f or -o ... didn't work as shown above.
Sample JSON blob object (from one Jenkins job). There are different Jenkins build job's JSON blob entries (each having different JSON structures, parameters etc) in a single JenkinsJobsBuild collection in MongoDB.
See attached for sample JSON blob object.
{
"_id": {
"$oid": "5120349es967yhsdfs907c4f"
},
"actions": [
{
"causes": [
{
"shortDescription": "Started by an SCM change"
}
]
},
{
},
{
"oneClickDeployPossible": false,
"oneClickDeployReady": false,
"oneClickDeployValid": false
},
{
},
{
},
{
},
{
"cspec": "element * ...\/MyProject_latest_int\/LATESTnelement * ...\/MyProject_integration\/LATESTnelement \/vobs\/some_vob\/gigi \/main\/myproject_integration\/MyProject_Slot_0_maint_int\/LATESTnelement * ...\/myproject_integration\/LATESTnelement \/vobs\/some_vob \/main\/LATEST",
"latestBlsOnConfiguredStream": null,
"stream": null
},
{
},
{
"parameters": [
{
"name": "CLEARCASE_VIEWTAG",
"value": "jenkins_MyProject_latest"
},
{
"name": "BUILD_DEBUG",
"value": false
},
{
"name": "CLEAN_BUILD",
"value": true
},
{
"name": "BASEVERSION",
"value": "7.4.1"
},
{
"name": "ARTIFACTID",
"value": "lowercaseprojectname"
},
{
"name": "SYSTEM",
"value": "myprojectSystem"
},
{
"name": "LOT",
"value": "02"
},
{
"name": "PIPENUMBER",
"value": "7.4.1.303"
}
]
},
{
},
{
},
{
"parameters": [
{
"name": "DESCRIPTION_SETTER_DESCRIPTION",
"value": "lowercaseprojectname_V7.4.1.303"
}
]
},
{
},
{
},
{
},
{
}
],
"artifacts": [
],
"building": false,
"builtOn": "servername",
"changeSet": {
"items": [
{
"affectedPaths": [
"vobs\/some_vob\/myproject\/apps\/app1\/Java\/test\/src\/com\/giga\/highlevelproject\/myproject\/schedule\/validation\/SomeActivityTest.java"
],
"author": {
"absoluteUrl": "http:\/\/11.22.33.44:8080\/user\/hitj1620",
"fullName": "name1, name2 A"
},
"commitId": null,
"date": {
"$numberLong": "1489439532000"
},
"dateStr": "13\/03\/2017 21:12:12",
"elements": [
{
"action": "create version",
"editType": "edit",
"file": "vobs\/some_vob\/myproject\/apps\/app1\/Java\/test\/src\/com\/giga\/highlevelproject\/myproject\/schedule\/validation\/SomeActivityTest.java",
"operation": "checkin",
"version": "\/main\/MyProject_latest_int\/2"
}
],
"msg": "",
"timestamp": -1,
"user": "user111"
}
],
"kind": null
},
"culprits": [
{
"absoluteUrl": "http:\/\/11.22.33.44:8080\/user\/nuka1620",
"fullName": "nuka, Chuck"
}
],
"description": "lowercaseprojectname_V7.4.1.303",
"displayName": "#303",
"duration": 525758,
"estimatedDuration": 306374,
"executor": null,
"fullDisplayName": "MyProject \u00bb MyProject-build #303",
"highlevelproject_metrics_source_url": "http:\/\/11.22.33.44:8080\/job\/MyProject\/job\/MyProject-build\/303\/\/api\/json",
"id": "303",
"keepLog": false,
"number": 303,
"projectName": "MyProject-build",
"queueId": 8201,
"result": "SUCCESS",
"timeToRepair": null,
"timestamp": {
"$numberLong": "1489439650307"
},
"url": "http:\/\/11.22.33.44:8080\/job\/MyProject\/job\/MyProject-build\/303\/"
}
When the regexes are in a file, you don't have to escape double quotes; you don't have to fight to get your double quotes past the shell.
"number":.*"projectName
"projectName":.*,"queueId
"queueId":.*,"result
"result":".*$
When that's fixed, I get:
$ egrep -o -f egrep-pattern.txt jsonfile.json
"number": 303,"projectName
"queueId":8881,"result
$
The trouble now is, I think, that you've consumed the projectName with the first pattern, so the others don't get a chance to match it. Change the patterns to read up to a comma and you can get better results:
"number":[^,]*
"projectName":[^,]*
"queueId":[^,]*
"result":".*$
yields:
"number": 303
"projectName": "giga"
"queueId":8881
"result":"SUCESS"}
You could try to be more delicate, but you rapidly reach a point where a JSON-aware tool becomes more sensible. Commas in a string value would mess up the modified regexes, for example. (So, if the project name was "Giga, if not Tera", you'd have problems.)
Matching more general JSON name:value notation
As long as you're looking for simple "key":"quoted value" objects, you can use the following grep -E (aka egrep) command:
grep -Eoe '"[^"]+":"((\\(["\\/bfnrt]|u[0-9a-fA-F]{4}))|[^"])*"' data
Given the JSON-like data (in the file called data):
{"key1":"value","key2":"value2 with \"quoted\" text","key3":"value3 with \\ and \/ and \f and \uA32D embedded"}
that script produces:
"key1":"value"
"key2":"value2 with \"quoted\" text"
"key3":"value3 with \\ and \/ and \f and \uA32D embedded"
You can upgrade it to handle almost any valid JSON "key":value by using:
grep -Eoe '"[^"]+":(("((\\(["\\/bfnrt]|u[0-9a-fA-F]{4}))|[^"])*")|true|false|null|(-?(0|[1-9][0-9]*)(\.[0-9]+)?([eE][-+]?[0-9]+)?))' data
With a new data file containing:
{"key1":"value","key2":"value2 with \"quoted\" text"}
{"key3":"value3 with \\ and \/ and \f and \uA32D embedded"}
{"key4":false,"key5":true,"key6":null,"key7":7,"key8":0,"key9":0.123E-23}
{"key10":10,"key11":3.14159,"key12":0.876,"key13":-543.123}
the script produces:
"key1":"value"
"key2":"value2 with \"quoted\" text"
"key3":"value3 with \\ and \/ and \f and \uA32D embedded"
"key4":false
"key5":true
"key6":null
"key7":7
"key8":0
"key9":0.123E-23
"key10":10
"key11":3.14159
"key12":0.876
"key13":-543.123
You can follow the railroad diagrams in the outline JSON specification at http://json.org to see how I created the regex.
It could be enhanced by the judicious addition of [[:space:]]* in places where spaces are permitted but not required — before the key string, before the colon, after the colon (you could add it after the value too, but you probably don't want that).
Another simplification that I've taken is that the key doesn't allow for the various escape characters that the value string does. You could repeat that.
And, of course, this only works for 'leaf' name:value pairs; if a value is itself an object {…} or an array […], this doesn't handle the value as a whole.
However, this just goes to emphasize that it gets very messy very quickly and you would be better off using a special-purpose JSON query tool. One such tool is jq, as mentioned in a comment to the main query.
The complex JSON blob I had, was from Jenkins (i.e. Jenkins job's RestAPI data) that I had in MongoDB database.
To grab it from MongoDB, I used mongoexport command for generating (non-JsonArray or non-Pretty format) JSON blob successfully.
#/bin/bash
server=localhost
collectionFile=collections.txt
## Generate collection file contains all collections in the Jenkins database in MongoDB.
( set -x
mongo "mongoDbServer.company.com/database_Jenkins" --eval "rs.slaveOk();db.getCollectionNames()" --quiet > ${collectionFile}
)
## create collection based JSON files
for collection in $(cat ${collectionFile} | sed -e 's:,: :g')
do
mongoexport --host ${server} --db ${db} --collection "${collection}" --out ${exportDir}/${collection}.json
##mongoexport --host ${server} --db ${db} --collection "${collection}" --type=csv --fieldFile ~/mongoDB_fetch/get_these_csv_fields.txt --out ${exportDir}/${collection}.csv; ## This didn't work if you have nested fields. fieldFile file was just containing field name per line in a particular xyz.IndexNumber.yyy format.
done
Tried inbuilt mongoexport command's --type=csv with -f fields to catch topfield.0.subField, field2, field3.7.parameters.7.. nothing worked.
PS: The number after the . mark is how you define indexes if you are going to create a CSV file and using fields (mandatory) using mongoexport command.
As my JSON structure was all unstructured (Jenkins version bumps/upgrades happened in past and the data about a job was not the same structure), I tried this final sed trick (as JSON data per entry was in each individual line).
This sed command (as shown below) will give you all the keys and it's values (in the key=value format) per line at the LEAF field key=value level of almost any JSON blob / at least from the Jenkins JSON blob . Once you have this info, you can feed the output of this command to temporary file, then read all the value part (after the = mark) and create your CSV file acc. YES, you have to sort it so that your CSV file's fields are maintained in order for the header names and thus values are inserted to the right column/field. I calculated the fields names from all different collection JSON file's temporary key=value generated key names. Then, read all temporary collection files and added the values acc. into the final CSV file under respective header/field/column.
OK this is a weird solution but at least it's a solution - in one liner.
cat myJenkinsJob.json | sed "s/{}//g;s/,,*/,/g;s/},\"/\n/g;s/},{/\n/g;s/\([^\"a-zA-Z]\),\"/\1\n/g;s/:\[{/\n/g;s/\"name\":\"//g;s/\",\"value//g;s/,\"/\n/g;s/\":\"*/=/g;s/\"//g;s/[\[}\]]//g;s/[{}]//g;s/\$[a-zA-Z][a-zA-Z]*=//g"|grep "=" | sed "s/,$//"|egrep -v "=-|=$|=\[|^_class="
Tweak this acc. to your own solution for the sed part a little bit, if your JSON blob shows you funny characters that you don't want. The order of sed operations below is important. I'm also excluding any redundant variables (that I don't need at this time, for ex: JSON blob contained _class="..." values) so I'm excluding those via egrep -v after the last | pipe.

Windows: curl with json data on the command line

I am running the following command in Windows prompt:
curl -XPUT http://127.0.0.1:9200/test-index/test-type/_mapping?pretty=true -d '{"test-type": {"properties": {"name": {"index": "analyzed", "term_vector": "with_positions_offsets", "boost": 1.0, "store": "yes", "type": "string"}}}}'
I get the following error:
{
"error" : "ElasticsearchParseException[Failed to parse content to map]; nested: JsonParseException[Unexpected character (''' (code 39)): expected a
valid value (number, String, array, object, 'true', 'false' or 'null')\n at [Source: org.elasticsearch.common.compress.lzf.LZFCompressedStreamInput#45
4ed1d2; line: 1, column: 2]]; ",
"status" : 400
}
I searched for solutions and found alternatives such as put json data in files, but I cannot use it for some reasons.
Thanks!
Windows's cmd doesn't support strings with single quotes. Use " and escape the inner ones with \".
"I searched for solutions and found alternatives such as put json data in files, but I cannot use it for some reasons"
This should work, with hello.json in temp. The # is requried.
c:\temp>curl -v -X PUT \
--data "#hello.json" \
-H "Content-Type:application/json" \
http://localhost:8080/api/myresource