Deepak wrote a couple of scripts for this. You have to install groovy
to run them. I would recommend sdkman http://sdkman.io/install.html ,
but any version should work.
https://github.com/GMOD/Apollo/blob/master/docs/web_services/examples/groovy/transfer_annotations2to2.groovy
https://github.com/GMOD/Apollo/blob/master/docs/web_services/examples/groovy/migrate_annotations1to2.groovy
Thanks. We have so few annotations at this point that we can migrate
manually.
Post by Nathan DunnI think we *may* have fixed that in 2.0.1, but either way, glad you found a fix for it.
If you need help migrating annotations between organisms let us know.
Nathan
I am using WA 2.0.0.
After looking at the stacktrace I think I found the problem. I had moved
the organism data directory to a different location on my server. I then
updated the filepath for the organism data file in WebApollo. From the
stacktrace it appears that WebApollo was still looking for some files in
the old (original) directory. To fix this, I simply created a new organism
and pointed it to the new directory location.
Thanks Nathan and Collin for your help!
Henry
Post by ColinJust to add to what Nathan said, it would be good to know which WA
version you're using as it could be a real error. That error often crops up
with corrupted annotations, specifically, orphaned features.
The basic idea behind the clue is that the "cfg" error that Henry
mentions is probably caused by this line in AnnotTrack.js
var cfg = this.config.style.alternateClasses[clsName];
So if whatever feature appears doesn't have a corresponding style in
the client/apollo/json/annot.json, then you get a null cfg there (often
times, due to it being an orphan and not a transcript type) then it causes
that error
The zoom level is probably a red herring as it would be showing up if
you zoomed in on the specifically corrupted feature too
-Colin
Post by Nathan DunnI had run into this a while ago. It disappears because it is
probably loading the last non-failing version. If you flush the cache (I
like to open a new âincognitoâ window), youâll probably see it again.
If you had a stack-trace of the error, that might be helpful. If you
had modified any aspect of the trackList.json to specifically configure the
annotations, that may also cause problems.
- ./apollo clean-all
- ./apollo deploy
will likely fix the problem as I seem to get this when not all of the
jbrowse libraries downloaded when I did the initial build.
Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
Post by Nathan HenryHello,
I have a problem with my User-created Annotations.
When I zoom out, the User-created Annotations track has an error.
Before I zoom out, I can zoom in, view, and edit the User-created
Annotations.
Post by Nathan HenryThe Diagnostic message is "TypeError: cfg is undefined".
After reloading the page, the track shows up again.
Has anyone experienced this error before?
Thank you for your time,
Henry
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