Error "Invalid RefObject was given: hg38" while following Tutorial 3

[rdbcasillas]

Hello,

I am following the Tutorial 3. Everything seems to be working except the last step which actually loads the GIVE browser.

After adding the html code to a new html file (last step) , when I go to http://myipaddress:40080/myindex.html, I get a "Warning" alert box. When I click on it multiple times, I get the following error in console:

refObject.js:513 Uncaught (in promise) Error: Invalid RefObject was given: hg38
    at Function.findRefByDb (refObject.js:513)
    at HTMLElement._setRefAfterReadyCheck (refEmbedMixin.js:118)
    at refEmbedMixin.js:82

I looked at refObject.js for that error but not sure what's the issue. I was able to initialize hg38 properly as specified in the tutorial.

Any help is greatly appreciated.

Thank you!

[HHG-biocode]

Running into the same area, curious if there is a solution you've found (error message in question): refObject.js:551 Uncaught (in promise) Error: Invalid RefObject was given: hg38 at Function.findRefByDb (refObject.js:551) at priorityManagerCollection.js:98 at Array.map () at priorityManagerCollection.js:85

[frankyan]

I just went through the tutorial 3 on a fresh machine again and didn't encounter any problem. I tried to reproduce your problem by setting some incorrect configurations. Although I couldn't reproduce the exact problems you encountered, a similar problem repeatedly showing warning alert box was caused by incorrectly setting server domain name using the command bash config_host.sh -r /var/www/give -d "http://give.genemo.org:40080" where you need to replace the domain name with your actual server's accessible domain name. If you can show all your command lines and the content of your final html file, I can help you to find the cause of your problem.

[HHG-biocode]

I ended up using the Custom Installation using MySQL (followed tutorial 3.2), so did not end up using GIVE-Docker commands for it. I'm checking my mysql configuration files at the moment --> did use the internal file location on a server and not the accessible domain name so might alter that to see what the effects are. My MySQL commands were taken from the manual section and tutorial 3.2, with a bigWig file added in.

[frankyan]

@HHG-biocode It's hard to reproduce and diagnose your problem if you are not using the standard GIVE-Docker. Because the dependent software and system environment might be totally different. Hence, I can only give you some suggestions.

The general cause of the problem is the data in your MySQL database cannot be correctly send to your client internet browser. There are two possible reasons: (1) failed server end communication between PHP and MySQL, (2) failed GIVE server access caused by incorrect GIVE domain name configuration.

Before diagnosing your problem, I suggest using the GIVE-Toolbox to configure your GIVE server and manage your data track, see tutorial 3 and manual GIVE-Toolbox usages. Although you are not using docker, you can still use GIVE-Toolbox which is a bundle of bash scripts can be found in the GIVE-Toolbox subfolder of this repo. It's much easier to do GIVE server management by using GIVE-Toolbox. If you really don't want to use GIVE-Toolbox, you'd better to read its tutorial and source code then you might understand the cause of your problem.

Perhaps you can check the following things:

• 1. You can use the list_tracks.sh tool on your server to see whether your MySQL data are accessible and correct. See the list_tracks.sh section in the manual and step 7 in the tutorial 3. If you cannot see the hg38 data imported, you need to check you MySQL and perhaps use GIVE-Toolbox to re-build you database.
• 2. If there isn't any problem in step 1, you can check the your GIVE data-hub webpage such as "http://YOURDOMAIN:YOURPORT/data-hub.htm". If you cannot see the correct information, it might indicate server end MySQL user/passwd setting or server domain name configuration problem.
• 3. Read the description and source code of GIVE-Toolbox config_host.sh. Then you can understand which files need to be edited if you don't want to use the config_host.sh tool.

Hope these suggestions can help you to solve the problem by yourself.

[HHG-biocode]

Followed your advice and use GIVE-Docker along with GIVE-Toolbox and have gotten past the issue. Thanks for the help!