Error loading genome comparison track into embeded browser

Tong-Chen commented 7 years ago

Thanks for this greatful genome browser for public and self usages.

The embeded browser worked well except when loading genome comparisn track.

The error is that base.js:7321 Uncaught TypeError: Cannot use 'in' operator to search for 'mm9' in undefined. But if I give this json hub file though URL, it worked.

I have tried to change showContext into datahub, same error.

Changing type: "genomealign" into filetype: "genomealign", no errors as well as no tracks loaded.

The core code is listed below:

    <div id="washu_browser" style="max-width: 1000px;margin-left: 75px"></div>
        <script type='text/javascript'>
            embed_washugb({
                host:'http://epigenomegateway.wustl.edu',
                container:document.getElementById('washu_browser'),
                genome:'hg19',

                showContent:[
                    {
                        name:"mm9tohg19",
                        type:'genomealign',
                        querygenome:'mm9',
                        url:'http://vizhub.wustl.edu/public/hg19/weaver/hg19_mm9_axt.gz',
                        reciprocal:{
                            hg19:'http://vizhub.wustl.edu/public/mm9/weaver/mm9_hg19_axt.gz',
                        },
                        mode:'show',
                        color:'#99004D',
                        tracks:[
                            {type:'native_track',list:[
                                {name:'refGene',mode:'full'},
                                {name:'SINE',mode:'full'}
                                ]
                            }
                        ]   
                    }
                ]
            });
        </script>
    </div>

Hope you can help to find out why. Thank you very much.

Chen Tong

Chinese Academy of Sciences

lidaof commented 7 years ago

Thanks @Tong-Chen for reporting this. I can reproduce this bug. Working on this and will let you know. Thanks again.

Tong-Chen commented 7 years ago

Would you get a chance to modify it? Thanks.

lidaof commented 7 years ago

Hi Chen,

We did look into it, still under fixing. Sorry for being slow, will keep you update.

On Sat, Jul 1, 2017 at 3:53 AM Chen Tong notifications@github.com wrote:

Would you get a chance to modify it? Thanks.

— You are receiving this because you were assigned.

Reply to this email directly, view it on GitHub https://github.com/epgg/eg/issues/59#issuecomment-312420146, or mute the thread https://github.com/notifications/unsubscribe-auth/AAGRlmGyV8ixDeuJPHYgvWpXUTKDzVEeks5sJgj4gaJpZM4N9aGS .

-- Daofeng

Tong-Chen commented 7 years ago

Daofeng, Thanks very much.

Tong

lidaof commented 7 years ago

sorry for late reply, this takes me a while to fix. in order to show the comparative track, need to include more js and I made some changes to embed.js as well. Please use the example below. Thanks.

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN"> 
<HTML> 
  <HEAD> 
    <TITLE>WashU Epigenome Browser</TITLE> 
    <link rel="stylesheet" type="text/css" href="http://epgg-test.wustl.edu/browser/css/style.css" />
    <script type="text/javascript" src="http://epgg-test.wustl.edu/browser/js/base.js"></script>
    <script type="text/javascript" src="http://epgg-test.wustl.edu/browser/js/session.js"></script>
    <script type="text/javascript" src="http://epgg-test.wustl.edu/browser/js/bev.js"></script>
     <script type="text/javascript" src="http://epgg-test.wustl.edu/browser/js/gsm.js"></script>
    <script type="text/javascript" src="http://epgg-test.wustl.edu/browser/js/session.js"></script>
    <script type="text/javascript" src="http://epgg-test.wustl.edu/browser/js/fileload.js"></script>
            <script type="text/javascript" src="http://epgg-test.wustl.edu/browser/js/scp.js"></script>
            <script type="text/javascript" src="http://epgg-test.wustl.edu/browser/js/geneplot.js"></script>
            <script type="text/javascript" src="http://epgg-test.wustl.edu/browser/js/validhub.js"></script>
        <script type="text/javascript" src="http://epgg-test.wustl.edu/browser/js/circlet.js"></script>
    <script type="text/javascript" src="http://epgg-test.wustl.edu/browser/js/sukn.js"></script>
    <script type="text/javascript" src="http://epgg-test.wustl.edu/browser/js/personality.js"></script>
    <script type="text/javascript" src="http://epgg-test.wustl.edu/browser/js/embed.js"></script>
    <script type="text/javascript" src="http://epgg-test.wustl.edu/browser/js/dataProvider.js"></script>
    <script type="text/javascript" src="http://epgg-test.wustl.edu/browser/js/hicInterface.js"></script>
  </head>

<body style='margin:20px;'>
<div id="washu_browser" style="max-width: 1000px;margin-left: 75px"></div>
        <script type='text/javascript'>
            embed_washugb({
                host:'http://epgg-test.wustl.edu',
                container:document.getElementById('washu_browser'),
                genome:'hg19',

                showContent:[
                    {
                        name:"mm9tohg19",
                        type:'genomealign',
                        querygenome:'mm9',
                        url:'http://vizhub.wustl.edu/public/hg19/weaver/hg19_mm9_axt.gz',
                        mode:'show',
                        color:'#99004D',
                        tracks:[
                            {type:'native_track',list:[
                            {name:'refGene',mode:'full'},
                            {name:'SINE',mode:'full'}
                            ]}
                        ]
                    }
                ]
            });
        </script>
    </div>

</body>
</html>

Tong-Chen commented 7 years ago

Daofeng, thank you very much for your work.

I will try to use it and give my feedback.

Thanks again.!

Tong

Tong-Chen commented 7 years ago

Daofeng, thank you ! It works as expected.

However, there are several minor issues you may have noticed.