PHP and MongoDB: Undefined index

Question

I am stuck in this complex looping through embedded documents. One of my embedded documents is formatted like this:

"BUSCO" : [
    {
        "short_summary_data" : {
            "Complete BUSCOs (C)" : "1411",
            "Complete and single-copy BUSCOs (S)" : "1397",
            "Complete and duplicated BUSCOs (D)" : "14",
            "Fragmented BUSCOs (F)" : "7",
            "Missing BUSCOs (M)" : "22",
            "Total BUSCO groups searched" : "1440"
        }
    },
    {
        "full_table" : {
            "EOG09360002" : {
                "status" : "Complete",
                "contig" : "Chr3",
                "start" : "430821",
                "end" : "448546",
                "score" : "7092.4",
                "length" : "3931"
            },
            "EOG0936000A" : {
                "status" : "Missing",
                "contig" : "",
                "start" : "",
                "end" : "",
                "score" : "",
                "length" : ""
            },
            "EOG0936001N" : {
                "status" : "Missing",
                "contig" : "",
                "start" : "",
                "end" : "",
                "score" : "",
                "length" : ""
            }
        }
    }
],

In my Laravel 5.2 application (PHP 5.2) I want to loop through the BUSCO.short_summary_data. Once, the "full_table" is in the embedded document, I can't loop through it. The code which I have now is only limited to looping through the short_summary_data and makes a table with the information.

@foreach ($id_array as $char)

    <?php
    $cursor = $collection->find(array("_id" => new MongoId($char)));
    ++$i;
    ?>
    @foreach ($cursor as $document)
            @if (!empty($document['BUSCO']))
                <p>These BUSCO statistics correspond to project number {{$i}}</p>
                @if (is_array($document['BUSCO']))
                    @foreach ($document['BUSCO'] as $BUSCO)
                        @if (is_array($BUSCO["short_summary_data"]))
                            @foreach ($BUSCO["short_summary_data"] as $key => $value)
                                <tr>
                                    <td>{{$key}}</td>
                                    <td>{{$value}}</td>
                                </tr>
                            @endforeach
                        @endif
                    @endforeach
                @endif
            @else
            @endif
        @endforeach
@endforeach

This code gives the error: Illegal string offset 'short_summary_data'. I am super stuck and don't know what the problem is!

Kevin Stich · Accepted Answer · 2016-12-01 15:56:45Z

1

Your BUSCO key's value is an array of arrays; one of which contains short_summary_data and one that does not. Can be seen by looking at the JSON [ and { layout here:

"BUSCO" : [
{
    "short_summary_data" : {
        "Complete BUSCOs (C)" : "1411",
        "Complete and single-copy BUSCOs (S)" : "1397",
        "Complete and duplicated BUSCOs (D)" : "14",
        "Fragmented BUSCOs (F)" : "7",
        "Missing BUSCOs (M)" : "22",
        "Total BUSCO groups searched" : "1440"
    }
},
{
    "full_table" : {
...

What's happening is you are getting to the entry inside $BUSCO that doesn't have the short_summary_data field (the object containing full_table) and it's throwing that warning.

@foreach ($document['BUSCO'] as $BUSCO)
    @if (isset($BUSCO["short_summary_data"]) && is_array($BUSCO["short_summary_data"]))

Note the added isset for this new conditional. The format in your post doesn't have a short_summary_data key in each $BUSCO piece of data, you need to check if it's there and to not proceed if that key is not set.

edited Dec 1, 2016 at 15:56

answered Dec 1, 2016 at 14:41

Kevin Stich

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4 Comments

Anna Jeanine Over a year ago

I have adjusted my code, now no error is shown but also no table :-(. Maybe you could help me with the formatting of my BUSCO embedded document, because I tried to get it like how you showed but it doesn't work for me. I use two separate queries to add the data

$collection->update(array("project_id" => $project_id), array('$push' => array('BUSCO' => array('short_summary_data' => $data))));

and

$collection->update(array("project_id" => $project_id), array('$push' => array('BUSCO' => array('full_table' => $data))));

. Do you know how to syntax to get the outcome you proposed?

Kevin Stich Over a year ago

Check this updated answer, I conflated the solution and another thought. Sorry!

Anna Jeanine Over a year ago

I have tried this, but now nothing is shown. When I remove the isset($BUSCO['short_summary_data"]) the undefined index error is thrown again.

Anna Jeanine Over a year ago

I fixed it! Thank you for helping me!

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