How to convert Perl generated string(Object) into JSON using PHP? - php

Question

I created a REST API using Laravel (Lumen). Basically I'm taking some values from database and need to do some functions. Here's the problem.
There's a field called web_data in my result set. It's Perl code. This is how it looks when I query the database using normal SQL editor like phpmyadmin and workbench.
{"caption" => "Genes (Comprehensive set from GENCODE 26)","colour_key" => "[biotype]","default" => {"MultiBottom" => "collapsed_label","MultiTop" => "gene_label","alignsliceviewbottom" => "as_collapsed_label","contigviewbottom" => "transcript_label","contigviewtop" => "gene_label","cytoview" => "gene_label"},"key" => "ensembl","label_key" => "[biotype]","multi_name" => "GENCODE 26 Comprehensive gene set","name" => "Comprehensive Gene Annotations from GENCODE 26"}
It's very clear and nothing wrong. But when I get the same result via my REST API, I'm getting the following output. It has many "\" symbols. Here's that output.
{\"caption\" => \"Genes (Comprehensive set from GENCODE 26)\",\"colour_key\" => \"[biotype]\",\"default\" => {\"MultiBottom\" => \"collapsed_label\",\"MultiTop\" => \"gene_label\",\"alignsliceviewbottom\" => \"as_collapsed_label\",\"contigviewbottom\" => \"transcript_label\",\"contigviewtop\" => \"gene_label\",\"cytoview\" => \"gene_label\"},\"key\" => \"ensembl\",\"label_key\" => \"[biotype]\",\"multi_name\" => \"GENCODE 26 Comprehensive gene set\",\"name\" => \"Comprehensive Gene Annotations from GENCODE 26\"}
Can you please tell me what's the reason for this? Is this an issue with PHP or something like that ?
And also I have another issue. This is Perl code containing "=>" symbols to seperate values. I need to convert this into a JSON object using PHP. Is that possible ?
Need to convert like following object.
{ "caption" : "Genes (Comprehensive set from GENCODE 26)", "colour_key" : "[biotype]", "default" : { "MultiBottom" : "collapsed_label" ...
This is the php code i'm using to create the REST output using SQL data.
public function testDualDatabaseConnection()
{
$testGene = DB::connection('mysql2')->select('select a.analysis_id, logic_name, ad.description, ad.display_label, ad.web_data FROM ( select distinct(analysis_id) as analysis_id from gene ) as a join analysis on (a.analysis_id = analysis.analysis_id) join analysis_description as ad on (analysis.analysis_id = ad.analysis_id) where ad.displayable = :wow1', ['wow1' => "1"]);
return response()->json($testGene);
}
And also this is the full JSON output i'm getting via REST API.
https://gist.github.com/chanakaDe/0d1e5916d8bc788bb101afa9b92dc9cd
In this response, you can see "web_data", that's also the part I need to convert to JSON again.

Answer 1

If on the off chance you really do have
{\"caption\" => \"Genes ...\", ...}
Then you have a JSON fragment, and the first you thing you need to do is turn it into a complete JSON document so it can be decoded.
$json_fragment_from_api = '{\"caption\" => \"Genes ...\", ...}';
$json_from_api = '{"result":"' . $json_fragment_from_api . '"}';
$response = json_decode($json_from_api, true);
$perl_code = $response["result"];
That said, I think it's far more likely that you only showed a portion of your actual input. You're far more likely to have received something that looks more like
{ "result": "{\"caption\" => \"Genes ...\", ...}" }
Since you already have a complete JSON document, simply start by decoding it.
$json_from_api = '{ "result": "{\"caption\" => \"Genes ...\", ...}" }';
$response = json_decode($json_from_api, true);
$perl_code = $response["result"];
At this point, you have the value from the database.
{"caption" => "Genes ...", ...}
That value is Perl code. More specifically, it's surely Perl code that was produced by Data::Dumper. This is going to be hard to convert into JSON.
You could use the following, but it won't handle everything:
$desired_json = str_replace(' =>', ':', $perl_code);
Here are some things it won't handle:
Undefined values
Strings containing =>
Strings containing $
Strings containing #
Strings containing non-ASCII or some non-printable characters.
As shown here:
$ perl -e'
use feature qw( say );
use Data::Dumper qw( Dumper );
local $Data::Dumper::Useqq = 1;
local $Data::Dumper::Terse = 1;
local $Data::Dumper::Indent = 0;
say(Dumper({ x => undef }));
say(Dumper({ x => " => " }));
say(Dumper({ x => q{$} }));
say(Dumper({ x => q{#} }));
say(Dumper({ x => "\x7F" }));
'
{"x" => undef} # Gives {"x": undef} instead of {"x": null}
{"x" => " => "} # Gives {"x": ": "} instead of {"x": " => "}
{"x" => "\$"} # Gives {"x": "\$"} instead of {"x": "$"}
{"x" => "\#"} # Gives {"x": "\#"} instead of {"x": "#"}
{"x" => "\177"} # Gives {"x": "\177"} instead of {"x": "\u007f"}

Answer 2

Not sure where that escaping happens (if you can, give some more details)
But, try to replace => with : and \" with " and you'll have yourself a valid json.
$string = '{\"caption\" => \"Genes (Comprehensive set from GENCODE 26)\",\"colour_key\" => \"[biotype]\",\"default\" => {\"MultiBottom\" => \"collapsed_label\",\"MultiTop\" => \"gene_label\",\"alignsliceviewbottom\" => \"as_collapsed_label\",\"contigviewbottom\" => \"transcript_label\",\"contigviewtop\" => \"gene_label\",\"cytoview\" => \"gene_label\"},\"key\" => \"ensembl\",\"label_key\" => \"[biotype]\",\"multi_name\" => \"GENCODE 26 Comprehensive gene set\",\"name\" => \"Comprehensive Gene Annotations from GENCODE 26\"}';
$string = str_replace('\"','"', $string);
$string = str_replace('=>',':', $string);
$json = json_decode($string, true);
print_r($json);
You can check it out here: https://3v4l.org/UBmGA
Apparently this answer got more hate than i'd expect. Nevertheless, it did help OP and i'm sticking by it. In the end, this is what SO stands for.
I would like to know though... why so many downvotes? I do take constructive criticism well and would like to know how to improve future answers.