Popup with error processing your 'trackList.json' file

[pwilx666]

I've encountered an error with one of the organisms we recently uploaded to Apollo. The error pops up with the message:

There was a problem processing your 'trackList.json' file: (TypeError) : null is not an object (evaluating 'vw(e,JUc).nc().a')

The tracks display ok, however adding new tracks or clicking on a tab in the Apollo GUI generates this error popup each time.

I checked the trackList.json file for the problem organism and it looks ok to me:

{"refSeqs":"seq/pfal3D7.fa.fai","tracks":[{"seqType":"dna","key":"Reference sequence","useAsRefSeqStore":true,"storeClass":"JBrowse/Store/SeqFeature/IndexedFasta","urlTemplate":"seq/pfal3D7.fa","category":"Sequence Analysis","label":"DNA","type":"SequenceTrack","faiUrlTemplate":"seq/pfal3D7.fa.fai"}],"names":{"url":"https://plasmodb.org/a/service/jbrowse/names/pfal3D7","type":"REST"},"include":["tracks.conf","dnaseq.json","rnaseq.json","chipseq.json","rnaseqJunctions.json","organismSpecific.json","functions.conf","apollo_gene_tracks.conf"]}

I also compared to an organism that doesn't generate the error message:

{"refSeqs":"seq/pfal7G8.fa.fai","tracks":[{"seqType":"dna","key":"Reference sequence","useAsRefSeqStore":true,"storeClass":"JBrowse/Store/SeqFeature/IndexedFasta","urlTemplate":"seq/pfal7G8.fa","category":"Sequence Analysis","label":"DNA","type":"SequenceTrack","faiUrlTemplate":"seq/pfal7G8.fa.fai"}],"names":{"url":"https://plasmodb.org/a/service/jbrowse/names/pfal7G8","type":"REST"},"include":["tracks.conf","dnaseq.json","rnaseq.json","chipseq.json","rnaseqJunctions.json","organismSpecific.json","functions.conf","apollo_gene_tracks.conf"]}There was a problem processing your 'trackList.json' file: (TypeError) : Cannot read property 'a' of null

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

Request URL: https://apollo.veupathdb.org/4514645602070511706990772972/jbrowse/data/trackList.json?v=0.5317250840568675
Request Method: GET
Status Code: 200
Remote Address: 128.192.21.20:443
Referrer Policy: no-referrer-when-downgrade
content-type: application/json
date: Tue, 13 Apr 2021 14:00:23 GMT
server: Apache/2.4.43 (Unix)
status: 200
:authority: apollo.veupathdb.org
:method: GET
:path: /4514645602070511706990772972/jbrowse/data/trackList.json?v=0.5317250840568675
:scheme: https
accept: /
accept-encoding: gzip, deflate, br
accept-language: en-GB,en-US;q=0.9,en;q=0.8
cache-control: no-cache
cookie: auth_probe=1; _ga=GA1.2.360568567.1615201116; auth_tkt=N2IwYjkxNTc0MzE1Y2YxNWZmZmJjOGMwZDViMTc5Mzc2MDZlYzE0YmFwaWRiIWFwaWRiITE2MTc4NzExNzk6; _gid=GA1.2.1281197396.1618241703; mod_auth_openidc_session=055eaccf-eb0f-4e06-8afa-393945eeb474; JSESSIONID=37B983113B230C27EC83CE73AD4E3586; _gat_Server0=1
pragma: no-cache
referer: https://apollo.veupathdb.org/4514645602070511706990772972/jbrowse/index.html?loc=Pf3D7_14_v3%3A0..3291936&tracklist=1
sec-fetch-dest: empty
sec-fetch-mode: cors
sec-fetch-site: same-origin
user-agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_16_0) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.129 Safari/537.36

The response is attached in response.txt

response.txt

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

[nathandunn]

@pwilx666 I'm not seeing anything explicit.

What happens if you remove the "include" and what happens if you remove "names"?

[nathandunn]

the other possibility is you can build with this and then report the error. Should be quite a bit more verbose:

diff --git a/build.xml b/build.xml
index e6d67604b..abf166cdf 100644
--- a/build.xml
+++ b/build.xml
@@ -39,8 +39,8 @@
             </classpath>
             <arg line="-war"/>
             <arg value="web-app"/>
-            <!--            <arg line="-style"/>-->
-            <!--            <arg value="PRETTY"/>-->
+                        <arg line="-style"/>
+                        <arg value="PRETTY"/>
             <!-- Additional arguments like -style PRETTY or -logLevel DEBUG -->
             <arg line="${gwt.args}"/>
             <arg value="org.bbop.apollo.gwt.Annotator"/>

[nathandunn]

Some further questions (adding on to what is above):

• What happens if you remove the "include" and what happens if you remove "names"?
• What happens if you use an incognito/private window ?
• what happens if you make the organism public and try to view that genome logged out?

FYI, this is the code where it is failing: https://github.com/GMOD/Apollo/blob/develop/src/gwt/org/bbop/apollo/gwt/client/TrackPanel.java#L911-L948 . . . my guess is that a type is being mis-specified.

You can definitely add debugging, etc. in there, as well if all else fails. Let me know what you find.