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Available Tracks Header Height Issue with metadata file #1240

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nathanhaigh opened this Issue Oct 24, 2018 · 4 comments

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nathanhaigh commented Oct 24, 2018

This issue only seems to only have appeared when I switched to using metadata file(s) for my tracks. It also seems to be somewhat intermittent or may go away with a rizes of the track hierarchy pane and page refresh.

Using the following:

  • JBrowse v1.15.4
  • Ubuntu with Firefox 62.0.3 (64-bit)

My trackList.json file contains:

"trackMetadata": {
      "sources": [
           { "type": "csv", "url": "my_metadata.csv" }
      ]
}

URL: http://crobiad.agwine.adelaide.edu.au/dawn/jbrowse/

It seems that on first load, the height of the div with id=dijit_layout_ContentPane_2 has a height and width set. The effect of the large height, is that the track hierarchy gets bumped down the page a long way:

image

Also, there is a div with id=dijit_layout_ContentPane_3 which has style="display: none;".

It seems that resizing the width of the track selection hierarchy pane and refreshing the page, results in the dijit_layout_ContentPane_2 div not having a height or width set and thus the "space" disappears. In addition, the dijit_layout_ContentPane_3 div is not created.

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nathanhaigh commented Nov 1, 2018

Has anyone had a chance to take a look at this yet @rbuels @cmdcolin ?

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cmdcolin commented Nov 2, 2018

Hadn't taken a look yet but it looks like this can be recreated if you make the modencode example use the Hierarchical track selector

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nathanhaigh commented Nov 2, 2018

Seem the height of the space is euqal to the height of the window when loaded. I had a bit of a poke around the JavaScript code and tried to do some debugging. I think when the Uncategorised track pane is generated it seems to be using an offsetHeight equal to the window height, in the following code block of ./src/JBrowse/View/TrackList/Hierarchical.js:

            onComplete: () => {
                // make a pane at the top to hold uncategorized tracks
                this.categories.Uncategorized = {
                    pane: new ContentPane({ className: 'uncategorized' }).placeAt( this.containerNode ),
                    tracks: {},
                    categories: {}
                };
                if( this.config.categoryOrder ) {
                    tracks = this.induceCategoryOrder(tracks, this.config.categoryOrder)
                }

                this.addTracks( tracks, true );

                // hide the uncategorized pane if it is empty
                if( ! this.categories.Uncategorized.pane.containerNode.children.length ) {
                    this.categories.Uncategorized.pane.domNode.style.display = 'none';
                }
            }
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cmdcolin commented Nov 23, 2018

Should be fixed on dev after #1253 merge

@cmdcolin cmdcolin closed this Nov 23, 2018

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