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bionanogenomics / JBrowsePlugin

JBrowse plugin to support BioNano Genomics files
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TypeError: Cannot use 'in' operator to search for 'name' #3

Open sauloal opened 8 years ago

sauloal commented 8 years ago

JBrowse: JBrowse-1.12.1

From: http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=101

Server: Python 2.7.11

python -m SimpleHTTPServer

Chrome: 49.0.2623.87 m (64-bit)

TypeError: Cannot use 'in' operator to search for 'name' in NeatHTMLFeatures(…) "TypeError: Cannot use 'in' operator to search for 'name' in NeatHTMLFeatures
    at .<anonymous> (http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:31:2)
    at .<anonymous> (http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:31:42)
    at j._milestoneFunction (http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:82:339)
    at j.initPlugins (http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:30:334)
    at http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:28:17
    at c (http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:165)
    at d (http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:91)
    at resolve (http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:238:145)
    at .<anonymous> (http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:84:421)
    at http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:141:23"
dojo.js:35 TypeError: Cannot use 'in' operator to search for 'name' in NeatHTMLFeatures
    at .<anonymous> (dojo.js:31)
    at .<anonymous> (dojo.js:31)
    at j._milestoneFunction (dojo.js:82)
    at j.initPlugins (dojo.js:30)
    at dojo.js:28
    at c (dojo.js:236)
    at d (dojo.js:236)
    at resolve (dojo.js:238)
    at .<anonymous> (dojo.js:84)
    at dojo.js:141

Firefox: 45.0.1

TypeError: invalid 'in' operand d[b]
... a))a.location="plugins/"+a.name;var b=this.resolveUrl(a.location);if(!("js"in a...
dojo.js (line 82)
.cache["JBrowse/Browser"]/</<.initPlugins/</d<@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:31:1
.cache["JBrowse/Browser"]/</<.initPlugins/<@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:30:473
.cache["JBrowse/Browser"]/</<._milestoneFunction@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:82:337
.cache["JBrowse/Browser"]/</<.initPlugins@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:30:1
.cache["JBrowse/Browser"]/</<.constructor/</<@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:28:15
.cache["dojo/Deferred"]/</c@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:165
.cache["dojo/Deferred"]/</d@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:91
.cache["dojo/Deferred"]/</k/this.resolve@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:238:145
.cache["JBrowse/Browser"]/</<.loadConfig/</<@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:84:419
.cache["dojo/_base/lang"]/</b.hitch/<@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:141:21
.cache["dojo/Deferred"]/</c@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:165
.cache["dojo/Deferred"]/</d@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:91
.cache["dojo/Deferred"]/</k/this.resolve@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:238:145
.cache["dojo/Deferred"]/</a@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:237:14
.cache["dojo/Deferred"]/</c@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:305
.cache["dojo/Deferred"]/</d@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:91
.cache["dojo/Deferred"]/</k/this.resolve@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:238:145
.cache["dojo/Deferred"]/</a@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:237:14
.cache["dojo/Deferred"]/</c@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:305
.cache["dojo/Deferred"]/</d@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:91
.cache["dojo/Deferred"]/</k/this.resolve@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:238:145
.cache["dojo/promise/all"]/</</</<@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:939:363
.cache["dojo/Deferred"]/</c@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:165
.cache["dojo/Deferred"]/</d@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:91
.cache["dojo/Deferred"]/</k/this.resolve@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:238:145
.cache["dojo/Deferred"]/</a@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:237:14
.cache["dojo/Deferred"]/</b/<@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:452
.cache["dojo/Deferred"]/</c@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:165
.cache["dojo/Deferred"]/</d@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:91
.cache["dojo/Deferred"]/</k/this.resolve@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:238:145
.cache["dojo/Deferred"]/</a@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:237:14
.cache["dojo/Deferred"]/</c@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:305
.cache["dojo/Deferred"]/</d@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:91
.cache["dojo/Deferred"]/</k/this.resolve@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:238:145
.cache["dojo/promise/all"]/</</</<@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:939:363
.cache["dojo/Deferred"]/</c@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:165
.cache["dojo/Deferred"]/</d@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:91
.cache["dojo/Deferred"]/</k/this.resolve@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:238:145
.cache["dojo/Deferred"]/</a@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:237:14
.cache["dojo/Deferred"]/</b/<@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:452
.cache["dojo/Deferred"]/</c@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:165
.cache["dojo/Deferred"]/</d@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:91
.cache["dojo/Deferred"]/</k/this.resolve@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:238:145
.cache["dojo/Deferred"]/</a@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:237:14
.cache["dojo/Deferred"]/</c@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:305
.cache["dojo/Deferred"]/</d@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:91
.cache["dojo/Deferred"]/</k/this.resolve@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:238:145
.cache["dojo/promise/all"]/</</</<@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:939:363
.cache["dojo/Deferred"]/</c@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:165
.cache["dojo/Deferred"]/</d@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:91
.cache["dojo/Deferred"]/</k/this.resolve@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:238:145
.cache["dojo/Deferred"]/</a@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:237:14
.cache["dojo/Deferred"]/</b/<@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:452
.cache["dojo/Deferred"]/</c@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:165
.cache["dojo/Deferred"]/</k/b.then@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:239:7
.cache["dojo/Deferred"]/</c@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:269
.cache["dojo/Deferred"]/</d@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:91
.cache["dojo/Deferred"]/</k/this.resolve@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:238:145
.cache["dojo/Deferred"]/</a@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:237:14
.cache["dojo/Deferred"]/</c@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:338
.cache["dojo/Deferred"]/</d@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:91
.cache["dojo/Deferred"]/</k/this.resolve@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:238:145
.cache["dojo/Deferred"]/</a@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:237:14
.cache["dojo/Deferred"]/</b/<@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:452
.cache["dojo/Deferred"]/</c@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:165
.cache["dojo/Deferred"]/</d@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:91
.cache["dojo/Deferred"]/</k/this.resolve@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:238:145
.cache["dojo/Deferred"]/</a@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:237:14
.cache["dojo/Deferred"]/</c@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:305
.cache["dojo/Deferred"]/</d@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:91
.cache["dojo/Deferred"]/</k/this.resolve@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:238:145
.cache["dojo/Deferred"]/</a@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:237:14
.cache["dojo/Deferred"]/</c@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:305
.cache["dojo/Deferred"]/</d@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:91
.cache["dojo/Deferred"]/</k/this.resolve@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:238:145
.cache["dojo/Deferred"]/</a@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:237:14
.cache["dojo/Deferred"]/</c@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:338
.cache["dojo/Deferred"]/</d@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:91
.cache["dojo/Deferred"]/</k/this.resolve@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:238:145
.cache["dojo/Deferred"]/</a@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:237:14
.cache["dojo/Deferred"]/</c@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:305
.cache["dojo/Deferred"]/</d@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:236:91
.cache["dojo/Deferred"]/</k/this.resolve@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:238:145
e@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:379:180
d@http://assembly.ab.wurnet.nl:8000/src/dojo/dojo.js:382:225
b(a=
TypeError: invalid 'in' operand d[b]

... a))a.location="plugins/"+a.name;var b=this.resolveUrl(a.location);if(!("js"in a...

)dojo.js (line 35)
.cache["JBrowse/Browser"]/</<.fatalError/<(c=Object { type="object"})dojo.js (line 36)
ma(a=Object { type="object"}, b=undefined)dojo.js (line 15)
ga/<()dojo.js (line 16)
la(a=Object { type="object"})dojo.js (line 15)
ga()dojo.js (line 16)
Fa/c(b="<div class="fatal_error"...:</h2>\n </div>\n</div>\n")dojo.js (line 16)
.cache["dojo/text"]/</<.load/h(a="<div class="fatal_error"...:</h2>\n </div>\n</div>\n")dojo.js (line 412)
.cache["dojo/text"]/</<.load/<(a="<div class="fatal_error"...:</h2>\n </div>\n</div>\n")dojo.js (line 412)
.cache["dojo/_base/xhr"]/</h._ioSetArgs/<(a="<div class="fatal_error"...:</h2>\n </div>\n</div>\n")dojo.js (line 363)
q()dojo.js (line 276)
n(a="<div class="fatal_error"...:</h2>\n </div>\n</div>\n")dojo.js (line 276)
.cache["dojo/_base/Deferred"]/</h.Deferred/this.callback(a="<div class="fatal_error"...:</h2>\n </div>\n</div>\n")dojo.js (line 277)
q()dojo.js (line 277)
n(a=Object { type="object"})dojo.js (line 276)
.cache["dojo/_base/Deferred"]/</h.Deferred/this.callback(a=Object { type="object"})dojo.js (line 277)
.cache["dojo/_base/xhr"]/</h.xhr/<()dojo.js (line 367)
.cache["dojo/Deferred"]/</c(c=Object { type="object"}, d=1, e="<div class="fatal_error"...:</h2>\n </div>\n</div>\n", f=null)dojo.js (line 236)
.cache["dojo/Deferred"]/</d(a=Object { type="object"}, b=1, d="<div class="fatal_error"...:</h2>\n </div>\n</div>\n", e=null, f=0)dojo.js (line 236)
.cache["dojo/Deferred"]/</k/this.resolve(a="<div class="fatal_error"...:</h2>\n </div>\n</div>\n", c=undefined)dojo.js (line 238)
.cache["dojo/Deferred"]/</a(a=Object { type="object"}, b=1, c="<div class="fatal_error"...:</h2>\n </div>\n</div>\n")dojo.js (line 237)
.cache["dojo/Deferred"]/</c(c=Object { type="object"}, d=1, e=Object { type="object"}, f=null)dojo.js (line 236)
.cache["dojo/Deferred"]/</d(a=Object { type="object"}, b=1, d=Object { type="object"}, e=null, f=0)dojo.js (line 236)
.cache["dojo/Deferred"]/</k/this.resolve(a=Object { type="object"}, c=undefined)dojo.js (line 238)
.cache["dojo/Deferred"]/</a(a=Object { type="object"}, b=1, c=Object { type="object"})dojo.js (line 237)
.cache["dojo/Deferred"]/</c(c=Object { type="object"}, d=1, e=Object { type="object"}, f=null)dojo.js (line 236)
.cache["dojo/Deferred"]/</d(a=Object { type="object"}, b=1, d=Object { type="object"}, e=null, f=0)dojo.js (line 236)
.cache["dojo/Deferred"]/</k/this.resolve(a=Object { type="object"}, c=undefined)dojo.js (line 238)
.cache["dojo/Deferred"]/</a(a=Object { type="object"}, b=1, c=Object { type="object"})dojo.js (line 237)
.cache["dojo/Deferred"]/</c(c=Object { type="object"}, d=1, e=Object { type="object"}, f=null)dojo.js (line 236)
.cache["dojo/Deferred"]/</d(a=Object { type="object"}, b=1, d=Object { type="object"}, e=null, f=0)dojo.js (line 236)
.cache["dojo/Deferred"]/</k/this.resolve(a=Object { type="object"}, c=undefined)dojo.js (line 238)
e(a=Object { type="object"}, b=undefined)dojo.js (line 379)
d()dojo.js (line 382)

..."error",innerHTML:b(a)+""},c)}else if(/^Could not load reference sequence/.test(...
sauloal commented 8 years ago

Fixed:

Download the plugin zip file wget -O 'JBrowsePlugin_20160322_9990bda.zip' https://github.com/bionanogenomics/JBrowsePlugin/archive/master.zip

Decompress the file: unzip JBrowsePlugin_20160322_9990bda.zip

Enter folder: cd JBrowsePlugin-master/

uncompress compiled plugin: unzip BioNanoGenomics.zip

move BioNanoGenomics folder to plugins folder: mv BioNanoGenomics JBrowse-1.12.1/plugins

@BionanoDev please correct https://github.com/bionanogenomics/JBrowsePlugin/wiki/BioNano-Genomics-Plugin-Installation accordingly if I'm correct

regards

sauloal commented 8 years ago

My mistake. I forgot to re-enable the plugin. still crashing. It seems that it only works with apache.

BionanoDev commented 8 years ago

Correct we used apache.

sauloal commented 8 years ago

I used python and node. neither worked.

BionanoDev commented 8 years ago

Thanks for testing that. Guess that is additional work to make sure it is compatible with those add'l web servers.

sauloal commented 8 years ago

help says that somewhere in the code you're requesting a JSON but the server is sending as text (not using magic mime type) and therefore DOJO is trying to use 'in' against a string instead of a object (parsed json). the solution being forcing the datatype (dataType: "JSON" for ajax, handleAs: "json" for xhr). I couldnt find where in the code you were requesting the JSON.

sauloal commented 8 years ago

Also doesnt work with NGINX in the jbrowse docker image

sauloal commented 8 years ago

I've tried with apache and found the same error

sauloal commented 8 years ago

I've succeeded in making it work by according to ( http://gmod.org/wiki/JBrowse_Configuration_Guide#Using_Plugins ), instead of using the .conf file, using the .json file:

{"plugins":["BioNanoGenomics"]}

this works without a problem

cmdcolin commented 7 years ago

There was a bug in previous jbrowse versions where if you declare plugins in trackList.json like"plugins": ["NeatHTMLFeatures"] and then in jbrowse.conf have the plugin declaration like

[plugins.BioNanoGenomics]
location=plugins/BioNanoGenomics

then it gave this error

Fixed in jbrowse 1.12.3 via https://github.com/GMOD/jbrowse/pull/866

cmdcolin commented 7 years ago

Note that there can still be weird behavior if you try to declare plugins in multiple files, so it's probably best to declare all plugins in jbrowse.conf, or all in trackList.json, but not a mix of both (which is what was probably the original cause of this issue). Ref https://github.com/GMOD/jbrowse/issues/897