some users can't update the gene name field

[Monica Poelchau]

Hi everyone, 

Some of our users have had trouble naming genes. Typically, when you change the name in a gene, a grey drop-down box will appear with the typed name. Once you select the name from the drop-down box, this name will be stored and displayed. The users having problems do not see the drop-down box. Consequently their gene name changes are not saved. They do not have problems changing the values of any other fields. Some users of this organism have the problem, others don't. I have sporadically observed this behavior myself but can't reproduce it consistently. 

Do you have an idea what might be going on? This is a show-stopping problem since the name field is important for this annotator group. 

Apollo info:

• Version: 2.6.5
• Grails version: 2.5.5
• Groovy version: 2.4.4
• JVM version: 1.8.0_322
• Servlet Container Version: Apache Tomcat/9.0.58
• JBrowse config: 1.16.11-release
• JBrowse url: https://github.com/GMOD/jbrowse
• Web Services

Browser info: The users reported using various browsers and experiencing the same problem. 

Thanks!

Monica

[Sofia Robb]

Hi Monica, 

By any chance do you also have problems with Synonyms/alias? I had similar issues with trying to supply aliases. No one could reproduce my issues but we came up with a solution that fixed my problems.

Sofia

On Mar 29, 2022, at 1:49 PM, Monica Poelchau <mpoe...@gmail.com> wrote:

Hi everyone, 

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[Monica Poelchau]

Hi Sofia,

So far nobody's reported problems with other fields. What was your solution? Thanks!

Monica

[Garrett Stevens]

Hi Monica,

Sofia's solution was (I think) the one proposed here: https://github.com/GMOD/Apollo/pull/2642. I couldn't reproduce the problem, though, so I couldn't properly review that PR. A few questions that might help me reproduce your problem: What is your deployment scenario? e.g. are you deploying with Docker or without? And what database are you using (MySQL or PostgreSQL)? I've tried to reproduce the problem on our demo server here: https://genomearchitect.readthedocs.io/en/latest/Demo.html, but wasn't able to. If you're able to reproduce it there it could help as well.

Best,

Garrett

[Sofia Robb]

Hi Monica,

Have you checked out your error messages? They might provide clues on what is going on. Mine were essentially: 

1. ERROR: null value in column "synonymsgml" violates not-null constraint
2. ERROR: null value in column "type_id" violates not-null constraint

- Sofia

[Sofia Robb]

Our issues were fixed by making a simple coding change and dropping some requirements in Chado. 

-sofia

[Monica Poelchau]

Thanks for the suggestions! I'll set up a session with the users to see if we can capture specific error messages. 

Incidentally, I just realized we can't add gene or mRNA aliases, either. I get the same error message that you do in the stacktrace when I try to add an mRNA alias. Oddly, I can't add a gene alias, either, but I don't get a stacktrace error then. 

[Sofia Robb]

Interesting. I don't think I ever tried adding a gene alias, only a transcript alias. And I can't remember if I tried to add a new gene name before I made changes to the code.

[Nathan Dunn]

I think the fix we did was:

alter table synonym alter column synonymsgml drop not null;

I can’t remember the exact error, but something like this on the server:

2022-02-18 17:41:22,272 [http-bio-8080-exec-83] ERROR StackTrace  - Full Stack Trace:
org.postgresql.util.PSQLException: ERROR: null value in column "synonymsgml" violates not-null constraint
  Detail: Failing row contains (166049, 0, test, null, null).
	at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2455)

Nathan

[Sofia Robb]

Yes, that is what we did, and everything we did is in the PR  https://github.com/GMOD/Apollo/pull/2642

[Monica Poelchau]

I got some new information about the gene naming error. When the user tried to add the gene name in Chrome (Version 99.0.4844.82 (Official Build) (64-bit)), the following console error pops up (nothing on the server logs). Note that this user can add a gene name in Safari or Edge. Other users can add the gene name in chrome.

annotator-0.js:3757 Uncaught
fvb {f: 'empty argument', g: null, __gwt$backingJsError: Error: empty argument
    at gj.dj [as Ib] (annotator-0.js:4308:31)
    at Wi (annotator-0.js:1228:…}
f: "empty argument"
g: null
__gwt$backingJsError: Error: empty argument at gj.dj [as Ib] (annotator-0.js:4308:31) at Wi (annotator-0.js:1228:26) at Ch (annotator-0.js:1944:25) at fvb.Jh (annotator-0.js:1231:25) at fvb.Lh (annotator-0.js:1073:19) at new fvb (annotator-0.js:1171:20) at ix (annotator-0.js:3757:77) at m7b.o7b [as gc] (annotator-0.js:4314:10606) at Bt (annotator-0.js:2984:79) at Qt.Rt [as ec] (annotator-0.js:4309:9936) at XMLHttpRequest.eval (annotator-0.js:2756:65) at qi (annotator-0.js:2013:29) at ti (annotator-0.js:2657:44) at XMLHttpRequest.eval (annotator-0.js:3472:50)
[[Prototype]]: Object

I've also attached a screenshot.

[Nathan Dunn]

Do you get this in Chrome in an Incognito window? 

If you could continue to expand that error, what do you see? 

Also, to clarify, was there an original gene name that you were changing, or had the existing gene lacked a name and you are adding one?

Nathan

<Apollo screen grab.png>

[Monica Poelchau]

Hi Nathan, 

- Do you get this in Chrome in an Incognito window?   - No, regular browsing.

- If you could continue to expand that error, what do you see? see screenshot

- Also, to clarify, was there an original gene name that you were changing, or had the existing gene lacked a name and you are adding one?

The gene had a standard NCBI pre-annotation name, XM_044412267.1, I was attempting to change it to the real name of the gene.

Thanks for your help with this!

[Garrett Stevens]

Hi Monica,

I think what Nathan was asking is when you encounter this problem, what happens if you then open a Chrome incognito window and try to do the same thing? If the problem persists in an incognito window, then we can narrow it down to something about Chrome on that computer (maybe version of Chrome or something). If there is no problem in the incognito window, then it's probably a problem with cookies or cache in Chrome.

Best,

Garrett

[Monica Poelchau]

Thanks for clarifying, Garrett! Naming a gene works in incognito mode. 

[Garrett Stevens]

Ok, good to know. That means that Chrome probably has something in its cache that is causing the problem. You can see here how to clear your cache: https://support.google.com/accounts/answer/32050. If you're unable to clear your whole cache for some reason, you can try the keyboard shortcut for "Reload the current page, ignoring cached content," which you can find for your OS here: https://support.google.com/chrome/answer/157179.

Best,

Garrett