Comment on this issue when beta is refreshed.

[kdahlquist]

I'm opening this issue so that you can post a comment here when the GRNsight beta server is refreshed, so that @kdahlquist (and others) will get an e-mail notification.

[NAnguiano]

The beta has been refreshed with the fix for issue #408. It also includes the tweaks from #397 and #395.

[NAnguiano]

Beta has been refreshed! It has issues #396 #397 #398 #399 and #419.

[NAnguiano]

For anyone who refreshes beta in the future, keep in mind that the node apps are now being run from the top directory, not the server and web-client directories. The apps are called using server/app.js and web-client/app.js. This is a direct result of the npm start implementation. npm start can't be used on the beta server itself because of the additional requirements, so running the apps on the parent directory is now required.

[NAnguiano]

Beta was refreshed with the new pull request just before the meeting. It included the fixes for #395,
#396, and #399.

[kdahlquist]

Did you increment the version number? Shouldn't we be on 2.0.3 now? I will look at it and post comments on the relevant issues.

[NAnguiano]

The version number is now properly incremented.

[NAnguiano]

Beta has been refreshed from PR #446 and #432.

[NAnguiano]

Beta has been refreshed from PR #448.

[NAnguiano]

Beta is refreshed from PR #459.

[kdahlquist]

Did Beta get refreshed from PR #460? It doesn't seem so.

[eileenchoe]

My bad -- it did not. I need to review how to refresh beta, I haven't actually done a refresh myself yet.

[kdahlquist]

Since you @anuvarsh, @NAnguiano, and @mihirsamdarshi seem to be working right now, will somebody refresh beta from PR #460 so it is up to date with the beta branch? Thanks.

[NAnguiano]

@kdahlquist @eileenchoe I updated it about 10 mins ago, so it should be up to date now!

[kdahlquist]

Got it!

[NAnguiano]

@eileenchoe I made a quick guide on the wiki to refresh the server right here. There's a more detailed guide on the wiki if you want to read it as well. :)

[NAnguiano]

beta has been refreshed

[dondi]

While the main beta line is in a pause as @NAnguiano finishes up, I figured it wouldn't hurt to upload the temporary normalization branch from @anuvarsh. This version, bumping to 2.0.17, includes the latest normalization implementation, including restoration of the previously lost functionality.

This version was branched from beta so all of the features from that branch as of May the 4th (be with you) should still be available anyway.

[dondi]

Beta points back to the beta branch now so it is at 2.0.16. If this branch is updated and changed, we should skip to 2.0.18 because normalization was inserted in between.

[kdahlquist]

Just noting that beta has been refreshed by @NAnguiano to 2.0.18.

[NAnguiano]

Beta is refreshed from PR #458 :)

[eileenchoe]

Beta refreshed from PR #486, #490, and #492!

[dondi]

The server update has been completed and GRNsight execution (both production and beta) has been restored. The beta page now shows v5.0.0 with today’s date.

I have also applied the new environment variables for connecting to the expression database on production, and in my testing that part now works.

The version of node on this latest Ubuntu server is indeed newer than the prior one, but still not the newest version (Ubuntu Long-Term-Service releases tend to skew very conservative in their version updates). I will see whether this new version is sufficient for the planned security updates. Stay tuned.

Final server uptime before reboot is as follows:

[dondi]

Following the merge of #985 the deployed beta is now at 6.0.2

A quick check seems to show a regression in database functionality though…genes that are appearing on prod do not seem to appear on beta now (for me). Maybe we can look at it at the meeting

[dondi]

Epic PR #996 has been merged into beta, which is now at 6.0.3

I have verified and closed the 6.0.2 regression bug #995 but have not had a chance to look into the other bugs on beta. If the team can please run beta through its paces in the next few days, we can close the remaining review requested items and potentially merge this into production

@Onariaginosa I think you had some follow-up commits relating to database scripting and documentation—all clear to do this

@Sarronnn you can now queue up your PR for #993 after merging beta into your branch (or maybe even starting a fresh branch from beta) and restoring the refactor work that you have done

[dondi]

Thanks to some quick-turnaround from @Onariaginosa, beta has been updated to 6.0.4 by way of #1004 being merged

[dondi]

PR #1025 has been merged into beta, bringing it to v6.0.6

[ahmad00m]

PR #1026 have been merged into beta. The version and modified date has been changed to reflect the new changes. beta is currently at v6.0.7

[Onariaginosa]

PR #1039 and #1040 has been merged into beta. The version and modified date has been updated. beta is now at v7.0.0

[dondi]

PR #1045, containing the fix for #1016, has been merged into beta. Version has been updated to v7.0.1

[dondi]

beta now has PR #1048 and PR #1049, holding fixes to #1033 and #1034

[dondi]

beta is now at 7.0.5, finally including PR #1037, which addresses #992. Local databases merging beta from this point will need to be revised accordingly

[dondi]

beta has been updated to 7.0.6 integrating PR #1063 to address issue #1050. Some notes have already been made on refining this fix further

[dondi]

beta is now on 7.0.7 integrating PR #1064 with refinements for issue #1050

[dondi]

beta is now on 7.0.8 integrating PRs #1073 and #1075 addressing issues #1072 and #1065 respectively

[dondi]

beta is now on 7.0.9 integrating @ceciliazaragoza’s code style changes address issue #1002

[akaiap]

beta is now on 7.0.12 integrating @ntran18 #1094

[ntran18]

beta is now on 7.0.13 integrating @ntran18 integrating PRs #1096 and #1101 to address issue #1079, #1097 to address issue #1054, and #1100 to fix issue #1099

[ceciliazaragoza]

beta is now on 7.0.14 integrating @ceciliazaragoza integrating PR #1109 and PR #1110 to address issue #1081 and @ntran18 integrating PR #1105 to address issue #1089.

[ceciliazaragoza]

beta is now on 7.0.15 integrating @ceciliazaragoza integrating PR #1112 and PR #1114 to address issue #1083 .

[dondi]

beta is now on 7.1.4 integrating PRs #1123, #1124, and #1125

[dondi]

beta has been updated to 7.1.5 with PRS #1127 and #1128

[dondi]

It took a little more time due to some delays on my part and additional review iterations, but beta is now at 7.1.6! PRs in this version include: #1129, #1131, #1132, #1133, #1134, #1136, and #1137. These PRs address issues #1080, #1130, #1059, #1093, #1098, #1068, #1107, #1108

That’s quite a few PRs and issues addressed—it’s truly bug-bash time 🐜🔨