Creating annotation stopped working in new version of Firefox (and Chrome)

[jasonsydes]

This is for Apollo 2.4.1 (the most recent).

• Provide what you were doing and what you expected to see. Screenshots, directory, config files are a plus if relevant.

Dragging and dropping a transcript from a track (see track info below) up to the User-created Annotations to create a new annotation doesn't work.

We were getting around that by right clicking on the transcript, then Create new annotation > gene I think yesterday that was not working in Chrome, but it definitely was working in Firefox. Since yesterday, our version of Firefox has been upgraded to the current version (70.0 (64-bit)). And now it does not work in Firefox.

Here's the first part of the transcript metadata:

Primary Data
Nameg741.t1
Typetranscript
Score0.01
Positiontig00000001|arrow:18142785..18243722 (- strand)
Length100,938 bp
Attributes
Idg741.t1
Seq_idtig00000001|arrow
SourceAUGUSTUS

Here's the track info:

{
  "maxFeatureSizeForUnderlyingRefSeq": 250000,
  "subfeatureDetailLevel": 2,
  "maxFeatureScreenDensity": 0.5,
  "enableCollapsedMouseover": false,
  "disableCollapsedClick": false,
  "maxFeatureGlyphExpansion": 500,
  "maxHeight": 600,
  "histograms": {
    "description": "feature density",
    "min": 0,
    "height": 100,
    "color": "goldenrod",
    "clip_marker_color": "red"
  },
  "style": {
    "_defaultHistScale": 4,
    "_defaultLabelScale": 30,
    "_defaultDescriptionScale": 120,
    "showLabels": true,
    "showTooltips": true,
    "label": "name,id",
    "description": "note, description",
    "className": "feature"
  },
  "displayMode": "normal",
  "events": {},
  "menuTemplate": [
    {
      "label": "View details",
      "title": "{type} {name}",
      "action": "contentDialog",
      "iconClass": "dijitIconTask"
    },
    {
      "iconClass": "dijitIconConnector"
    },
    {
      "iconClass": "dijitIconFilter"
    },
    {
      "label": "Create new annotation",
      "children": [
        {
          "label": "gene"
        },
        {
          "label": "pseudogene"
        },
        {
          "label": "tRNA"
        },
        {
          "label": "snRNA"
        },
        {
          "label": "snoRNA"
        },
        {
          "label": "ncRNA"
        },
        {
          "label": "rRNA"
        },
        {
          "label": "miRNA"
        },
        {
          "label": "Repeat region"
        },
        {
          "label": "Terminator"
        },
        {
          "label": "Transposable element"
        }
      ]
    }
  ],
  "storeClass": "JBrowse/Store/SeqFeature/NCList",
  "urlTemplate": "tracks/augustus_Z_final/{refseq}/trackData.jsonz",
  "label": "augustus_Z_final",
  "apollo": {
    "topType": "transcript",
    "source": "upload",
    "type": "GFF3_JSON_CANVAS"
  },
  "type": "WebApollo/View/Track/WebApolloNeatCanvasFeatures",
  "key": "augustus_Z_final",
  "baseUrl": "https://someplace.edu/apollo/207729112159036141748219796/jbrowse/data/",
  "index": 6,
  "metadata": {}
}

• Provide the javascript console log output generated from the action.

In both Firefox and Chrome: 1.bundle.js:1 biotype not found [transcript] converting to mRNA

• Provide the server log output generated from the action (typically catalina.out).

There is no server log generated from this action (confirmed by carefully watching tail -f localhost_access_log.2019-10-25.txt localhost.2019-10-25.log catalina.out catalina.2019-10-25.log).

Thank you for Apollo!!

[nathandunn]

@jasonsydes

I am able to do this with Firefox 70 and Chrome Version 78.0.3904.70 (Official Build) (64-bit), both on Mac.

1 - What do you see on the network tab?

You should either see websockets (preferably) messages (pictured) or XHR output when you create an annotation. If you could copy and paste the sent and received parts.

2 - Can you create an annotation off of the canvas tracks here?

http://demo.genomearchitect.org/Apollo2/annotator/loadLink?loc=ctgA:9047..14920&organism=228544&tracks=CDS

demo@demo.com / demo

3 - Does it work on Safari and/or on incognito windows in Firefox or Chrome? Does it work if you do a hard reset of the cache.

[jasonsydes]

Hi @nathandunn, good to chat with you! So, this is mainly what I'm seeing on the javascript console:

When I do the Network tab, this is what I see:

Safari

Firefox (incognito): Nothing

Chrome (incognito):

Basically, I think the only thing I see showing up on the Network tab is when I initially right-click on the annotation (sometimes, but not all the time). But when I click on "gene" (i.e. the last step to create a user-created annotation) nothing shows up on the Network tab.

This seems to be the same with Safari/Firefox/Chrome... (I haven't had time to reset cache on any of these.)

I am able to create annotations on your demo site just fine. For example, on regular (not-ingognito Chrome):

So it seems like this is something funky with our annotations somehow? I will say that I get the same behavior whether I'm trying to create an annotation based off of Augustus GFF annotation, or these track types: WebApollo/View/Track/WebApolloAlignments2 OR WebApollo/View/Track/WebApolloNeatCanvasFeatures.