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Jolene and Toni have reported problems duplicating genes on Apollo. Checking the logs revealed the JSONObject not found error. This was replicated on several phage organisms (T5, C2, PBSX, ZW6) on both Jolene's and Toni's user account.

10/22/2018 2:26:15 PM2018-10-22 19:26:15,545 [clientInboundChannel-2] ERROR springwebsocket.GrailsSimpAnnotationMethodMessageHandler - Unhandled exception
10/22/2018 2:26:15 PMjava.lang.reflect.InvocationTargetException
10/22/2018 2:26:15 PM at org.bbop.apollo.AnnotationEditorController$__do_annotationEditor_closure4$_closure5$_closure6.doCall(AnnotationEditorController.groovy:1144)
10/22/2018 2:26:15 PM at org.bbop.apollo.AnnotationEditorController$__do_annotationEditor_closure4$_closure5.doCall(AnnotationEditorController.groovy:1143)
10/22/2018 2:26:15 PM at org.bbop.apollo.AnnotationEditorController$__do_annotationEditor_closure4.doCall(AnnotationEditorController.groovy:1139)
10/22/2018 2:26:15 PM at groovyx.gpars.group.PGroup$3.call(PGroup.java:289)
10/22/2018 2:26:15 PM at groovyx.gpars.group.PGroup$4.run(PGroup.java:313)
10/22/2018 2:26:15 PM at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
10/22/2018 2:26:15 PM at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
10/22/2018 2:26:15 PM at java.lang.Thread.run(Thread.java:748)
10/22/2018 2:26:15 PMCaused by: org.codehaus.groovy.grails.web.json.JSONException: JSONObject["name"] not found.
10/22/2018 2:26:15 PM at org.bbop.apollo.FeatureService._do_generateTranscript(FeatureService.groovy:193)
10/22/2018 2:26:15 PM at org.bbop.apollo.RequestHandlingService.$tt__addTranscript(RequestHandlingService.groovy:651)
10/22/2018 2:26:15 PM ... 8 more

@jrr-cpt reports getting the following error messages on occasion when dragging the boundaries on gene feature annotations, but after clicking through the message the change appears to have been made anyway.

Perhaps something is getting called twice for the operation or a delay/race condition in the database update is causing a momentary desync of the database?

cc @jrr-cpt

For example:

Some confusion is caused by updates to the mRNA name are displayed in Apollo but later processing steps use the gene feature name.

Possible fixes:

• Copy changes to gene name to mRNA name when changed(we used to do this in our old version via hacky steps on the annotation editor popup)
• Configurable in Apollo to display/edit gene feature names instead of displaying mRNA names
• Post-retrieval tool configurable to rename mRNA/gene to match
• Change the retrieval process to rename mRNA and gene to be matching (unideal)

From @RyYoung

Currently the retrieve data from APollo has an option to retrieve the peptide sequences. This is good but each fasta is listed with the hash ID rather than the gene name. Would be much better if at least the option of having each fasta element listed with the name.

I think this is something that could be improved and worked on in future sprints. Logging it here for now

Right-clicking on a gene feature in Apollo to edit the annotation and you see

The order should be shuffled so that Edit Information is closer to the top. If the Edit Information option can be renamed to something that sounds more like 'make annotation' and helps people realize that is the one to click (rather than CPT GO Annotation), that would also be helpful.

When leaving comments in popup window for any feature in Apollo, these would not be saved properly. Even if typed, then the mouse was clicked off to 'save', and the window was closed then re-opened, then the comments would not be present. This was a common complaint for students in BICH464.

It is a known issue for overlapping features.

It may also be triggered when leaving comments with special characters.

When attempting to move the boundaries for any gene feature called from the Sixpack evidence track, nothing occurs visually and the following error message is in the logs.

2018-11-02 21:08:38,135 [clientInboundChannel-1] ERROR springwebsocket.GrailsSimpAnnotationMethodMessageHandler - Unhandled exception
java.lang.reflect.InvocationTargetException
at org.bbop.apollo.AnnotationEditorController$__do_annotationEditor_closure4$_closure5$_closure6.doCall(AnnotationEditorController.groovy:1144)
at org.bbop.apollo.AnnotationEditorController$__do_annotationEditor_closure4$_closure5.doCall(AnnotationEditorController.groovy:1143)
at org.bbop.apollo.AnnotationEditorController$__do_annotationEditor_closure4.doCall(AnnotationEditorController.groovy:1139)
at groovyx.gpars.group.PGroup$3.call(PGroup.java:289)
at groovyx.gpars.group.PGroup$4.run(PGroup.java:313)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NullPointerException: Cannot get property 'id' on null object
at org.bbop.apollo.FeatureService.$tt__convertFeatureToJSON(FeatureService.groovy:1686)
at org.bbop.apollo.RequestHandlingService._do_setExonBoundaries(RequestHandlingService.groovy:1018)
... 8 more

Is it possible to get Apollo to allow searching for AA sequences within protein sequences? The window has a search tab but it always says no database or somesuch. I wanted to find the pentapeptide sequence NYADI because that was the center of homology with another protein.

(Copied over from CPT/Galaxy-tools from @RyYoung )

Original 2.0.X patch was diffed onto the current GMOD master branch and included into the docker-apollo image for use on Rancher. cpt.tamu.edu/apollo-testing is the location of the testing version

Testing will proceed until ready for production. As of the version pushed on 10-5-2018, these are the problems reported from testing:

Jolene:

1. The name of the gene does not update on the screen when I click outside the box or hit tab. I can close the popup menu and move around with no apparent change to the name. But if I refresh the page it did save the change and displays correctly. CONFIRMED
2. Some random name changes I made to a phage in the apollo-testing did actually show up in my organism in the 'old/live' Apollo. As did my new called features. WILL DOUBLE CHECK, SHOULD HAVE SEPARATE DATA STORES
3. When I try to create a new feature, either a gene or a tRNA, it also does not update in the annotation track until I refresh the page. Actually I had to try several times before it did add the feature. This was the case for all three gene caller tracks. Did allow me to delete the feature and it was removed from the annotation track after a refresh. **CONFIRMED
4. As usual, cannot drag boundaries of sixpack features. UNTESTED

@MoffMade @BeaverThing Noticed an error in the coordinates that are generated in the gff3 for a feature when two genes that are in the same reading frame are called. Usually this happens when we are comparing the possible lengths for a particular gene: we call both, check the nucleotides in the start and SD, then delete one. What I noticed in the Spanins Test Genome organism is that if you called the longer possible ORF first, then ended up deleting it, the shorter feature still had the gene coordinates of the longer feature, though child coordinates are correct. I can reproduce this error by simple order of calling and deleting.

For example, I noticed that the output of this OSP tool in the evidence track was extending the feature out in the 5' direction from the start.

This was actually correct because the gff3 for the feature had the longer coordinates:

And by deleting the gene, then calling the MGA (light blue) feature, followed by the Glimmer (dark blue/shorter) feature, both features end up with the same gene coordinates. Then it doesn't matter which gets deleted, because the coordinates are already set.

Perhaps a good question for Apollo/Nathan?

Apollo supports authentication options for remote user authentication as part of the apollo-config.groovy. We need to expose this option as an environment variable flag for docker.