Re: [Gmod-ajax] Callback function error with dbxrefs

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

 No worries, I'm glad you found this workaround.

it is actually really good to hear about any issues people might have with
CLI so we can potentially find ways to fix.

I know nodejs isn't very common in bioinformatics so for some people
installing jbrowse CLI is people's first experience with nodejs, so we want
to make sure it's easy. I considered possibly making a single file binary
version of jbrowse CLI for example

-Colin

On Tue, Dec 12, 2023 at 2:37 PM Vaneet Lotay <van...@uc...>
wrote:

> Sorry this dragged on so long Colin.  So I find out that when using ‘npm
> install -g’ it installs the @jbrowse/cli tool in 3 different places when
> I’m using sudo or root user.  One of the places “/usr/local/bin/jbrowse”
> was the old v2.6.3 while the other two were the latest v2.9.  So I removed
> the symlink that was in /usr/local/bin, which actually points to a
> directory under /usr/local/lib.  Afterwards when trying to run the jbrowse
> command it unfortunately only looks in the /usr/local/bin/ directory again,
> even though the other two locations where the v2.9.0 was installed are
> clearly in my PATH.  Anyways I simply recreated that symlink under
> /usr/local/bin for JBrowse but pointed it to one of the v2.9.0 executables
> in the other location.  Now when checking the version I get the right
> release #:
>
>
>
> jbrowse --version
>
> @jbrowse/cli/2.9.0 linux-x64 node-v20.10.0
>
>
>
> Hopefully, this workaround functions ok when I upgrade the client tool in
> the future, I’ll have to see.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> *From:* Colin <col...@gm...>
> *Sent:* Monday, December 11, 2023 5:29 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] Callback function error with dbxrefs
>
>
>
> [△EXTERNAL]
>
>
>
> I was mostly referring to how you installed the @jbrowse/cli tool
>
>
>
> I think because you have a version of @jbrowse/cli in "/usr/lib/" because
> that is listed by npm list -g in your previous post, which suggests to me
> that you have used "sudo npm install -g @jbrowse/cli" or run "npm install
> -g @jbrowse/cli" under a root or privileged account. This is ok. And, that
> one looks like the latest correct version. But, you might also have another
> version installed somewhere else too, and that is the v2.6.3 version. Try
> identifying where that v2.6.3 version is installed perhaps, with commands
> like "which jbrowse" or npm list -g like mentioned previously. And then you
> can try uninstalling that version (npm uninstall -g @jbrowse/cli is a valid
> command)
>
>
>
> Hope that helps :)
>
>
>
> -Colin
>
>
>
> On Mon, Dec 11, 2023 at 7:12 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hey Colin,
>
>
>
> Are you referring to how I installed npm or Node.js? Or how I
> installed/unpacked JBrowse2? I believe JBrowse2 was done under my user but
> perhaps npm was installed using root. I'll have to double check but I
> suppose that can cause some discrepancies.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> Get Outlook for Android <https://aka.ms/AAb9ysg>
> ------------------------------
>
> *From:* Colin <col...@gm...>
> *Sent:* Monday, December 11, 2023 4:40:06 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li... <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] Callback function error with dbxrefs
>
>
>
> [△EXTERNAL]
>
>
>
> The note that you made about running as root may be a clue. You might have
> somehow installed it twice, once as a root user, and once as a non-root
> user. I would just try to be consistent, e.g. always use the root account
> (or equivalently basically, always use "sudo jbrowse ...") or always
> unpriviledged. There may be some way to "only install as a root, and then
> run the rest of the time as a non-root user" but I can't necessarily advise
> on all the cases on how this may affect. You might have installed a version
> as a non-root user, for example, my email above actually is an example of
> that, my library is in
>
> /home/cdiesh/.fnm/node-versions/v20.10.0/installation/lib because I use
> "fnm" for managing multiple node versions and so that could be where your
> v2.6.3 is coming from, and that shadows the system version of v2.9.0
>
>
>
>
>
>
>
>
>
> On Mon, Dec 11, 2023 at 4:47 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hey Colin,
>
>
>
> I get the same output from the ‘npm install’ command as you except that
> it’s “changed 297 packages” instead of added so I assume it’s working but
> the version check doesn’t show the new version number.  Perhaps this might
> give more of a clue to what’s going on, when I run the ‘npm list’ command I
> get this:
>
>
>
> XenJBrowse2# npm list -g
>
> /usr/lib
>
> ├── @jbrowse/cli@2.9.0
>
> ├── corepack@0.22.0
>
> └── npm@10.2.3
>
>
>
> Interesting that here it lists the latest JBrowse release #, but I’m not
> seeing that change in my main JBrowse 2 folder.  Does this give any other
> clue to what might be going on?  I need to switch to root when running the
> npm install command to have access to the full suite of npm commands, but
> not sure if that conflicts with anything here.
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
> *From:* Colin <col...@gm...>
> *Sent:* Friday, December 8, 2023 3:29 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] Callback function error with dbxrefs
>
>
>
> [△EXTERNAL]
>
>
>
> Hi there,
>
> Running the "npm install -g @jbrowse/cli" should get the latest version,
> so then, running "jbrowse --version" should report the latest version
> (currently, 2.9.0)
>
>
>
> So for me
>
>
>
> % npm install -g @jbrowse/cli
>
> added 297 packages in 12s
>
> 45 packages are looking for funding
>   run `npm fund` for details
>
> ~ took 12s
> % jbrowse --version
> @jbrowse/cli/2.9.0 linux-x64 node-v20.10.0
>
>
>
> I am not sure why this is not happening in your case. You can try running
>
>
>
> "npm list -g"
>
>
>
> This will list globally installed npm packages and their locations. So for
> me, it outputs a folder named
>
>
>
> /home/cdiesh/.fnm/node-versions/v20.10.0/installation/lib
>
>
>
> And then a folder in that same directory is where all the binaries that
> are in your path should be
>
>
>
> /home/cdiesh/.fnm/node-versions/v20.10.0/installation/bin
>
>
>
> If you have manually manipulated your PATH variable to try to add npm
> binaries to your PATH, you might consider adjusting that or removing the
> custom PATH for npm entirely (it should be automatic under most
> installations)
>
>
>
> Note: we removed the gt gff3 -sortlines because it outputted inaccurate
> sorting that would be rejected by tabix under certain circumstances. There
> was also an awk command and this also was bugged. We replaced it with a new
> built-in jbrowse CLI command, the sort-gff
>
>  to try to avoid the external dependency and make it easier to run
> (hopefully!)
>
>
>
> Let me know if that helps
>
> -Colin
>
>
>
> On Fri, Dec 8, 2023 at 2:53 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hey Colin,
>
>
>
> Speaking of changes to the doc pages, I noticed someone might have changed
> the tutorial page for adding JBrowse tracks? This page:
>
>
>
>
> https://jbrowse.org/jb2/docs/quickstart_web/#adding-a-gff3-file-with-gff3tabix
>
>
>
> I believe it used to say ‘gt gff3 …..’ for the command to initially sort
> the gff3.  Now it uses the ‘jbrowse sort-gff’ command which I don’t seem to
> have in my release of JBrowse tools.  This relates to my issue.  I
> attempted to upgrade JBrowse to the latest release, also it because has
> some addons/fixes I’m interested in, but it didn’t seem to work.  I used
> these commands from the tutorial page:
>
>
>
> jbrowse upgrade
>
> npm install -g @jbrowse/cli
>
>
>
> I didn’t receive any errors.  However when I try the new jbrowse sort-gff
> command it’s not found.  My version is still listed as such:
>
>
>
> jbrowse --version
>
> @jbrowse/cli/2.6.3 linux-x64 node-v20.9.0
>
>
>
> Do you know if I’m missing something needed to upgrade to the latest
> release?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> *From:* Vaneet Lotay <van...@uc...>
> *Sent:* Monday, November 27, 2023 4:41 PM
> *To:* Colin <col...@gm...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] Callback function error with dbxrefs
>
>
>
> [△EXTERNAL]
>
>
>
> That was the issue for me, thank you for fixing this! My dbxref links work
> fine now.
>
>
>
> Vaneet
>
>
>
> *From:* Colin <col...@gm...>
> *Sent:* Monday, November 27, 2023 3:43 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] Callback function error with dbxrefs
>
>
>
> [△EXTERNAL]
>
>
>
> I made a code fix to this link
> https://jbrowse.org/jb2/docs/config_guides/customizing_feature_details/#example-a-generalized-solution-to-dbxrefs
> just yesterday after I saw this thread, the diff was
>
>
>
>
>
> old
>
>   ;(typeof self !== 'undefined' ? self : window).JBrowsePluginMyPlugin = {
>     default: Plugin, // this variable "Plugin" wasn't defined
>   }
>
>
>
> new
>
>
>
>
>   ;(typeof self !== 'undefined' ? self : window).JBrowsePluginMyPlugin = {
>     default: MyPlugin, // fixed! this refers to class MyPlugin. change to
> DbxrefPlugin or whatever the name of your class is
>   }
>
>
>
> On Mon, Nov 27, 2023 at 4:59 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hey Colin,
>
>
>
> Thanks I did catch that mistake for the plugin name, which I forgot to
> change in one place.  Now I’ve got this error in the browser:
>
>
>
> TypeError: Illegal constructor.
>
>
>
> I tried to see what could be causing this but haven’t located it yet. Any
> ideas?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
>
>
> *From:* Colin <col...@gm...>
> *Sent:* Sunday, November 26, 2023 8:03 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] Callback function error with dbxrefs
>
>
>
> [△EXTERNAL]
>
>
>
> Hi there
>
> I think if you copied from here
> https://jbrowse.org/jb2/docs/config_guides/customizing_feature_details/#example-a-generalized-solution-to-dbxrefs
> then also have to rename JBrowsePluginMyPlugin ->
> JBrowsePluginDbxrefPlugin. You can see that the error message is looking
> for that variable name because that is what you named it in your
> config.json (it looks for the name JBrowsePlugin+name from the
> config.json), so I think that should help
>
>
>
> -Colin
>
>
>
>
>
> Footnote: it is definitely a little tricky that you have to meticulously
> have the right name for the plugin in so many places. Hopefully in the
> future it might not require this if we switch to so called "esm plugins".
> ESM plugins are already supported by jbrowse 2 but some browsers don't have
> great support for them yet, so they aren't our default example in the
> documentation, but we may update our examples to them in the future
>
>
>
> On Thu, Nov 23, 2023 at 3:15 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hi all,
>
>
>
> I followed the same structure that was outlined in the docs section at
> jbrowse.org (‘generalized solution to dbxrefs’) with different content
> obviously.  I created a dbxrefPlugin.js file with a ‘linkout’ function
> under a plugin named DbxrefPlugin.  When trying to load the genome for
> which I’m attempting to use the callback function I see this error:
>
>
>
> *Failed to load UMD bundle for DbxrefPlugin, JBrowsePluginDbxrefPlugin is
> undefined*
>
>
>
> Any idea where I’m going wrong?  I can attach some code if it’s not
> something simple or obvious I’m missing here.
>
>
>
> Just at the preliminary stages of trying to understand how JBrowse2
> functions behind the scenes, so I may have other moments like this in the
> future 😊
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
>
>
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