Tabular data not displaying in main panel

2 Oct 2013

      Hi all,

Multiple users of our internal Galaxy server have reported with
multiple browsers that tabular data is not displayed in the main
central panel. The preview in the history works, but clicking on
the "eye" icon gives a blank page.

I can confirm this in Firefox 24.0 and Safari 6.0.5, the HTML
for the central frame looks blank but is actually a script when
viewed via the frame source. The tabular file data is there in
the script's first_data_chunk entry - but does not get shown.
An except is shown below.

Has anyone else noticed this problem? I believe it began
when I last updated this Galaxy instance, but was not
noticed immediately.

Thanks,

Peter

-----------------------

I believe we are running the current stable release, or at least
the latest commit on the default branch from galaxy-dist

$ hg pull
warning: bitbucket.org certificate with fingerprint
24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not
verified (check hostfingerprints or web.cacerts config setting)
real URL is https://bitbucket.org/galaxy/galaxy-dist
pulling from http://bitbucket.org/galaxy/galaxy-dist
searching for changes
no changes found

$ hg update
0 files updated, 0 files merged, 0 files removed, 0 files unresolved

$ hg branch
default

[galaxy@ppserver galaxy-dist]$ hg log -b default | head
changeset:   10411:c42567f43aa7
user:        greg
date:        Mon Aug 19 13:19:56 2013 -0400
summary:     Filter invalid objects when generating the list of
repository_dependencies objects that are associated with a tool shed
repository installed into Galaxy.

changeset:   10410:e9ee9c5d30ae
user:        Dave Bouvier <dave@bx.psu.edu>
date:        Mon Aug 19 13:08:45 2013 -0400
summary:     Remove duplicate method from the install and test's
functional_tests.py.
...

-----------------------

<!DOCTYPE HTML>
<html>
    <!--base.mako-->
    <head>
        <title>Dataset Display</title>
        <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />

    <link href="/galaxy/static/style/base.css?v=1380731103"
media="screen" rel="Stylesheet" type="text/css" />

    <script src="/galaxy/static/scripts/libs/jquery/jquery.js?v=1380731103"
type="text/javascript"></script>
<script src="/galaxy/static/scripts/libs/jquery/jquery.migrate.js?v=1380731103"
type="text/javascript"></script>
<script src="/galaxy/static/scripts/libs/jquery/select2.js?v=1380731103"
type="text/javascript"></script>
<script src="/galaxy/static/scripts/libs/bootstrap.js?v=1380731103"
type="text/javascript"></script>
<script src="/galaxy/static/scripts/libs/underscore.js?v=1380731103"
type="text/javascript"></script>
<script src="/galaxy/static/scripts/libs/backbone/backbone.js?v=1380731103"
type="text/javascript"></script>
<script src="/galaxy/static/scripts/libs/backbone/backbone-relational.js?v=1380731103"
type="text/javascript"></script>
<script src="/galaxy/static/scripts/libs/handlebars.runtime.js?v=1380731103"
type="text/javascript"></script>
<script src="/galaxy/static/scripts/galaxy.base.js?v=1380731103"
type="text/javascript"></script>

    <script src="/galaxy/static/scripts/templates/compiled/template-popupmenu-menu.js?v=1380731103"
type="text/javascript"></script>

    <script src="/galaxy/static/scripts/mvc/ui.js?v=1380731103"
type="text/javascript"></script>

    <script type="text/javascript">
        // console protection
        window.console = window.console || {
            log     : function(){},
            debug   : function(){},
            info    : function(){},
            warn    : function(){},
            error   : function(){},
            assert  : function(){}
        };

        // Set up needed paths.
        var galaxy_paths = new GalaxyPaths({
            root_path: '/galaxy/',
            image_path: '/galaxy/static/images'
        });
    </script>

    <script src="/galaxy/static/scripts/libs/require.js?v=1380731103"
type="text/javascript"></script>
    <script src="/galaxy/static/scripts/templates/compiled/helpers-common-templates.js?v=1380731103"
type="text/javascript"></script>

    <script type="text/javascript">
        require.config({
            baseUrl: "/galaxy/static/scripts",
            shim: {
                "libs/backbone/backbone": { exports: "Backbone" },
                "libs/backbone/backbone-relational": ["libs/backbone/backbone"]
            }
        });

        require(['mvc/data'], function(data) {
            data.createTabularDatasetChunkedView(
                _.extend( {"misc_blurb": "7,891 lines", "peek":
"<table cellspacing=\"0\"
cellpadding=\"3\"><tr><th>1</th><th>2</th><th>3</th></tr><tr><td>Gpa_EST_02_04___C05_022</td><td>GO:0005737</td><td>...</td></tr></table>",
"data_type": "tabular", "deleted": false, "history_id":
"cdbf837ba6516a14", "metadata_column_names": null, "visible": true,
"genome_build": "?", "hid": 10, "file_size": 509095,
"metadata_data_lines": 7891, "file_ext": "tabular", "id":
"0ddcd2cf2375e24a", "misc_info": "\nBLASTX output identified\nInput
has 4507 queries\nDone\nStandard out:\nBlast2GO Pipeline Version
2.5.0\n--------------------------------------\n\nHash for resource
ec2go_19072011.txt of type ec created. 4003 associations
loaded.\nBlast2GO build: 23092011\nChange ", "hda_ldda": "hda",
"name": "Blast2GO Local database (May 2011)", "metadata_columns": 3,
"uuid": null, "state": "ok", "metadata_comment_lines": null,
"model_class": "HistoryDatasetAssociation", "metadata_dbkey": "?",
"purged": false, "metadata_column_types": ["str", "str", "str"]},
                        {
                            url_viz: "/galaxy/visualization",
                            chunk_url:
"/galaxy/dataset/display?dataset_id=0ddcd2cf2375e24a",
                            first_data_chunk: {"ck_index": 1,
"ck_data": "Gpa_EST_02_04___C05_022\tGO:0005737\tn-dimethylarginine
dimethylaminohydrolase\n...\n"}
                        }
                ),
                // Append view to body.
                $('body')
            );
        });
    </script>

    </head>
    <body>

    </body>
</html>

--

Peter Cock

Björn Grüning

sam guerler

Hans-Rudolf Hotz

Peter Cock

sam guerler

Peter Cock

Peter Cock

Eric Rasche

sam guerler

Björn Grüning

Peter Cock

Eric Rasche

Peter Cock

Peter Cock

Eric Rasche

Peter Cock

Peter Cock

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