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

Question

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\/"
}

Answer 1

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.

Answer 2

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.